dbSNP rs3814700: ADM-DT:n.744A>G (chr11-10303111-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000847672.1(ADM-DT):n.744A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,252 control chromosomes in the GnomAD database, including 607 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 0.072 ( 606 hom., cov: 33)

Exomes 𝑓: 0.066 ( 1 hom. )

Consequence

ADM-DT
ENST00000847672.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

Publications

4 publications found

Variant links:

Genes affected

ADM-DT (HGNC:55516): (ADM divergent transcript)

ADM-DT links:

SBF2 (HGNC:2135): (SET binding factor 2) This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]

SBF2 Gene-Disease associations (from GenCC):

Charcot-Marie-Tooth disease type 4B2
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, ClinGen, Ambry Genetics

SBF2 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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
SBF2	NM_001424318.1 link	c.-3+185A>G	intron_variant	Intron 1 of 40	NP_001411247.1
SBF2	NM_001425070.1 link	c.-3+1389A>G	intron_variant	Intron 1 of 40	NP_001411999.1
SBF2	NM_001425069.1 link	c.-3+1389A>G	intron_variant	Intron 1 of 39	NP_001411998.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ADM-DT	ENST00000847672.1 link	n.744A>G	non_coding_transcript_exon_variant	Exon 1 of 1
ADM-DT	ENST00000526906.2 link	n.562-61A>G	intron_variant	Intron 1 of 1	2
SBF2	ENST00000685217.1 link	n.386+1381A>G	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0716

AC:

10884

AN:

151906

Hom.:

603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0265

Gnomad AMI

AF:

0.0747

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.0542

Gnomad FIN

AF:

0.0563

Gnomad MID

AF:

0.0605

Gnomad NFE

AF:

0.0775

Gnomad OTH

AF:

0.0805

GnomAD4 exome

AF:

0.0658

AC:

AN:

228

Hom.:

Cov.:

AF XY:

0.0592

AC XY:

AN XY:

152

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.118

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0595

AC:

AN:

168

Other (OTH)

AF:

0.0500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0716

AC:

10889

AN:

152024

Hom.:

606

Cov.:

AF XY:

0.0720

AC XY:

5352

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.0264

AC:

1095

AN:

41460

American (AMR)

AF:

0.118

AC:

1802

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0510

AC:

177

AN:

3470

East Asian (EAS)

AF:

0.280

AC:

1435

AN:

5134

South Asian (SAS)

AF:

0.0542

AC:

261

AN:

4814

European-Finnish (FIN)

AF:

0.0563

AC:

596

AN:

10582

Middle Eastern (MID)

AF:

0.0719

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0775

AC:

5268

AN:

67966

Other (OTH)

AF:

0.0787

AC:

166

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

512

1023

1535

2046

2558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0808

Hom.:

242

Bravo

AF:

0.0756

Asia WGS

AF:

0.142

AC:

492

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

-0.84

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over