dbSNP rs9914220: SOCS3-DT:n.401-384C>T (chr17-78366809-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000592569.1(SOCS3-DT):n.401-384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,270 control chromosomes in the GnomAD database, including 2,574 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 0.15 ( 2574 hom., cov: 33)

Consequence

SOCS3-DT
ENST00000592569.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Publications

18 publications found

Variant links:

Genes affected

SOCS3-DT (HGNC:52799): (SOCS3 divergent transcript)

SOCS3-DT 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS3-DT	NR_110847.1 link	n.406-384C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SOCS3-DT	ENST00000592569.1 link	n.401-384C>T	intron_variant	Intron 2 of 4	3
SOCS3-DT	ENST00000794147.1 link	n.587-384C>T	intron_variant	Intron 3 of 4
SOCS3-DT	ENST00000794148.1 link	n.428-384C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22208

AN:

152152

Hom.:

2566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.0209

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0623

Gnomad OTH

AF:

0.138

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.146

AC:

22251

AN:

152270

Hom.:

2574

Cov.:

AF XY:

0.144

AC XY:

10734

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.296

AC:

12276

AN:

41538

American (AMR)

AF:

0.126

AC:

1933

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

454

AN:

3470

East Asian (EAS)

AF:

0.386

AC:

1998

AN:

5172

South Asian (SAS)

AF:

0.154

AC:

744

AN:

4828

European-Finnish (FIN)

AF:

0.0209

AC:

222

AN:

10624

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0623

AC:

4235

AN:

68022

Other (OTH)

AF:

0.145

AC:

307

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

909

1817

2726

3634

4543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.0853

Hom.:

1567

Bravo

AF:

0.164

Asia WGS

AF:

0.248

AC:

864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

(source)

DANN

Benign

0.59

PhyloP100

-0.16

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over