dbSNP rs79928962: NSD1:c.927+48A>G (chr5-177136078-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_022455.5(NSD1):c.927+48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,451,320 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 33 hom., cov: 32)

Exomes 𝑓: 0.026 ( 546 hom. )

Consequence

NSD1
NM_022455.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.11

Publications

2 publications found

Variant links:

Genes affected

NSD1 (HGNC:14234): (nuclear receptor binding SET domain protein 1) This gene encodes a protein containing a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The encoded protein enhances androgen receptor (AR) transactivation, and this enhancement can be increased further in the presence of other androgen receptor associated coregulators. This protein may act as a nucleus-localized, basic transcriptional factor and also as a bifunctional transcriptional regulator. Mutations of this gene have been associated with Sotos syndrome and Weaver syndrome. One version of childhood acute myeloid leukemia is the result of a cryptic translocation with the breakpoints occurring within nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1 on chromosome 5 and nucleoporin, 98-kd on chromosome 11. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Sep 2018]

NSD1 Gene-Disease associations (from GenCC):

Beckwith-Wiedemann syndrome due to NSD1 mutation
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
Sotos syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen
Sotos syndrome 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics

NSD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 5-177136078-A-G is Benign according to our data. Variant chr5-177136078-A-G is described in ClinVar as Benign. ClinVar VariationId is 261599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0182 (2779/152284) while in subpopulation NFE AF = 0.0282 (1921/68020). AF 95% confidence interval is 0.0272. There are 33 homozygotes in GnomAd4. There are 1333 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 2779 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022455.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NSD1	NM_022455.5	MANE Select	c.927+48A>G	intron	N/A	NP_071900.2
NSD1	NM_001409301.1		c.927+48A>G	intron	N/A	NP_001396230.1
NSD1	NM_001409302.1		c.927+48A>G	intron	N/A	NP_001396231.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NSD1	ENST00000439151.7	TSL:1 MANE Select	c.927+48A>G	intron	N/A	ENSP00000395929.2
NSD1	ENST00000347982.9	TSL:1	c.54+48A>G	intron	N/A	ENSP00000343209.5
NSD1	ENST00000602285.1	TSL:1	n.1147A>G	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2782

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00446

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.00832

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0301

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0283

Gnomad OTH

AF:

0.0129

GnomAD2 exomes

AF:

0.0213

AC:

4779

AN:

224242

AF XY:

0.0222

show subpopulations

Gnomad AFR exome

AF:

0.00514

Gnomad AMR exome

AF:

0.00790

Gnomad ASJ exome

AF:

0.0146

Gnomad EAS exome

AF:

0.0000631

Gnomad FIN exome

AF:

0.0317

Gnomad NFE exome

AF:

0.0274

Gnomad OTH exome

AF:

0.0214

GnomAD4 exome

AF:

0.0259

AC:

33592

AN:

1299036

Hom.:

546

Cov.:

AF XY:

0.0261

AC XY:

17057

AN XY:

653030

show subpopulations

African (AFR)

AF:

0.00361

AC:

106

AN:

29378

American (AMR)

AF:

0.00820

AC:

357

AN:

43546

Ashkenazi Jewish (ASJ)

AF:

0.0143

AC:

358

AN:

25078

East Asian (EAS)

AF:

0.00

AC:

AN:

37664

South Asian (SAS)

AF:

0.0305

AC:

2467

AN:

81000

European-Finnish (FIN)

AF:

0.0311

AC:

1609

AN:

51718

Middle Eastern (MID)

AF:

0.0348

AC:

184

AN:

5288

European-Non Finnish (NFE)

AF:

0.0282

AC:

27342

AN:

970756

Other (OTH)

AF:

0.0214

AC:

1169

AN:

54608

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1497

2994

4492

5989

7486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

950

1900

2850

3800

4750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0182

AC:

2779

AN:

152284

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1333

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.00445

AC:

185

AN:

41566

American (AMR)

AF:

0.00831

AC:

127

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00979

AC:

AN:

3472

East Asian (EAS)

AF:

0.000578

AC:

AN:

5188

South Asian (SAS)

AF:

0.0267

AC:

129

AN:

4826

European-Finnish (FIN)

AF:

0.0301

AC:

319

AN:

10606

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0282

AC:

1921

AN:

68020

Other (OTH)

AF:

0.0128

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

139

278

418

557

696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0167

Hom.:

Bravo

AF:

0.0151

Asia WGS

AF:

0.0150

AC:

AN:

3476

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

2.1

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over