chr17-38375739-T-C

Variant names:

• chr17-38375739-T-C
• rs8074124
• NM_014598.4:c.1553-1975T>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.1553-1975T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,942 control chromosomes in the GnomAD database, including 7,430 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 (7430 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SOCS7 NM_014598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS7	NM_014598.4	c.1553-1975T>C		intron_variant	Intron 6 of 9	ENST00000612932.6	NP_055413.2
SOCS7	XM_017024551.2	c.1451-1975T>C		intron_variant	Intron 5 of 8		XP_016880040.1
SOCS7	XM_017024552.2	c.1346-1975T>C		intron_variant	Intron 4 of 7		XP_016880041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS7	ENST00000612932.6	c.1553-1975T>C		intron_variant	Intron 6 of 9	1	NM_014598.4	ENSP00000482229.2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43006 AN: 151824 Hom.: 7408 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.283 AC: 43066 AN: 151942 Hom.: 7430 Cov.: 32 AF XY: 0.280 AC XY: 20830 AN XY: 74272

African (AFR) AF: 0.482 AC: 19972 AN: 41396

American (AMR) AF: 0.206 AC: 3136 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3464

East Asian (EAS) AF: 0.432 AC: 2234 AN: 5170

South Asian (SAS) AF: 0.270 AC: 1295 AN: 4802

European-Finnish (FIN) AF: 0.179 AC: 1889 AN: 10580

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12904 AN: 67974

Other (OTH) AF: 0.288 AC: 605 AN: 2104

Alfa AF: 0.216 Hom.: 6839

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs8074124; hg19: chr17-36531565;