rs9914196

Variant names:

• chr17-78366787-C-A
• rs9914196
• ENST00000592569.1:n.401-406C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-78366787-C-A
• chr17-78366787-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592569.1(SOCS3-DT):​n.401-406C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,218 control chromosomes in the GnomAD database, including 2,569 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 (2569 hom., cov: 33)
• Consequence: SOCS3-DT ENST00000592569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.401-406C>A		intron_variant	Intron 2 of 4	3
SOCS3-DT	ENST00000794147.1	n.587-406C>A		intron_variant	Intron 3 of 4
SOCS3-DT	ENST00000794148.1	n.428-406C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22293 AN: 152100 Hom.: 2561 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22336 AN: 152218 Hom.: 2569 Cov.: 33 AF XY: 0.145 AC XY: 10775 AN XY: 74422

African (AFR) AF: 0.296 AC: 12284 AN: 41518

American (AMR) AF: 0.127 AC: 1935 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5170

South Asian (SAS) AF: 0.154 AC: 743 AN: 4818

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10614

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4317 AN: 68016

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.113 Hom.: 211

Bravo AF: 0.164

Asia WGS AF: 0.248 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.47
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs9914196; hg19: chr17-76362868;