NM_014598.4:c.1682-2058T>C

Variant names:

• chr17-38393251-T-C
• rs12051836
• NM_014598.4:c.1682-2058T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014598.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS7	NM_014598.4	MANE Select	c.1682-2058T>C		intron	N/A	NP_055413.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS7	ENST00000612932.6	TSL:1 MANE Select	c.1682-2058T>C		intron	N/A	ENSP00000482229.2
	SOCS7	ENST00000665913.1		c.1490-2058T>C		intron	N/A	ENSP00000499750.1
	SOCS7	ENST00000613678.5	TSL:5	c.1403-2058T>C		intron	N/A	ENSP00000484381.2

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

African (AFR) AF: 0.565 AC: 23416 AN: 41418

American (AMR) AF: 0.199 AC: 3034 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5168

South Asian (SAS) AF: 0.145 AC: 701 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10592

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10957 AN: 68000

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.137 Hom.: 414

Bravo AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12051836; hg19: chr17-36549504;