17-38393251-T-C

Position:

• chr17-38393251-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014598.4(SOCS7):​c.1682-2058T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,060 control chromosomes in the GnomAD database, including 8,318 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 0.28 (8318 hom., cov: 32)
• Consequence: SOCS7 NM_014598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

SOCS7 (HGNC:29846): (suppressor of cytokine signaling 7) Predicted to enable 1-phosphatidylinositol-3-kinase regulator activity. Predicted to be involved in phosphatidylinositol phosphate biosynthetic process. Predicted to act upstream of or within several processes, including brain development; fat cell differentiation; and insulin receptor signaling pathway. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

SOCS7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOCS7	NM_014598.4	c.1682-2058T>C		intron_variant		ENST00000612932.6	NP_055413.2
SOCS7	XM_017024551.2	c.1580-2058T>C		intron_variant			XP_016880040.1
SOCS7	XM_017024552.2	c.1475-2058T>C		intron_variant			XP_016880041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOCS7	ENST00000612932.6	c.1682-2058T>C		intron_variant		1	NM_014598.4	ENSP00000482229.2
SOCS7	ENST00000665913.1	c.1490-2058T>C		intron_variant				ENSP00000499750.1
SOCS7	ENST00000613678.5	c.1403-2058T>C		intron_variant		5		ENSP00000484381.2
SOCS7	ENST00000617360.1	n.1931-6262T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41876 AN: 151942 Hom.: 8288 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.276 AC: 41944 AN: 152060 Hom.: 8318 Cov.: 32 AF XY: 0.269 AC XY: 20007 AN XY: 74354

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.277

Alfa AF: 0.137 Hom.: 414

Bravo AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12051836; hg19: chr17-36549504;