dbSNP rs17151639: SND1:c.1779+6707A>G (chr7-127997763-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014390.4(SND1):c.1779+6707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 534,584 control chromosomes in the GnomAD database, including 17,633 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 7261 hom., cov: 32)

Exomes 𝑓: 0.22 ( 10372 hom. )

Consequence

SND1
NM_014390.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79

Publications

16 publications found

Variant links:

Genes affected

SND1 (HGNC:30646): (staphylococcal nuclease and tudor domain containing 1) This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016]

SND1 links:

SND1-IT1 (HGNC:24158): (SND1 intronic transcript 1)

SND1-IT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014390.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SND1	NM_014390.4	MANE Select	c.1779+6707A>G		intron	N/A	NP_055205.2	Q7KZF4
	SND1-IT1	NR_027330.1		n.255A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SND1	ENST00000354725.8	TSL:1 MANE Select	c.1779+6707A>G	intron	N/A	ENSP00000346762.3	Q7KZF4
SND1	ENST00000903603.1		c.1937+6707A>G	intron	N/A	ENSP00000573662.1
SND1	ENST00000915268.1		c.1869+6707A>G	intron	N/A	ENSP00000585327.1

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44370

AN:

151998

Hom.:

7257

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.397

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.0485

Gnomad SAS

AF:

0.0898

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.309

GnomAD2 exomes

AF:

0.222

AC:

55910

AN:

251360

AF XY:

0.216

show subpopulations

Gnomad AFR exome

AF:

0.429

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.322

Gnomad EAS exome

AF:

0.0429

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.216

AC:

82686

AN:

382468

Hom.:

10372

Cov.:

AF XY:

0.206

AC XY:

44814

AN XY:

217724

show subpopulations

African (AFR)

AF:

0.423

AC:

4445

AN:

10512

American (AMR)

AF:

0.189

AC:

6874

AN:

36306

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

3773

AN:

11744

East Asian (EAS)

AF:

0.0444

AC:

585

AN:

13176

South Asian (SAS)

AF:

0.0936

AC:

6246

AN:

66764

European-Finnish (FIN)

AF:

0.178

AC:

5741

AN:

32320

Middle Eastern (MID)

AF:

0.289

AC:

825

AN:

2854

European-Non Finnish (NFE)

AF:

0.260

AC:

49982

AN:

192064

Other (OTH)

AF:

0.252

AC:

4215

AN:

16728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3843

7686

11528

15371

19214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.292

AC:

44399

AN:

152116

Hom.:

7261

Cov.:

AF XY:

0.281

AC XY:

20865

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.424

AC:

17580

AN:

41466

American (AMR)

AF:

0.255

AC:

3898

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

1155

AN:

3470

East Asian (EAS)

AF:

0.0484

AC:

251

AN:

5188

South Asian (SAS)

AF:

0.0903

AC:

435

AN:

4816

European-Finnish (FIN)

AF:

0.177

AC:

1874

AN:

10578

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18092

AN:

67992

Other (OTH)

AF:

0.310

AC:

654

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1606

3211

4817

6422

8028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.279

Hom.:

13742

Bravo

AF:

0.309

Asia WGS

AF:

0.100

AC:

349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.28

(source)

DANN

Benign

0.24

PhyloP100

-2.8

Mutation Taster

=100/0

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

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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