rs905078571

Variant names:

• chr17-38352860-C-G
• NM_014598.4:c.808C>G

Your query was ambiguous. Multiple possible variants found:

• chr17-38352860-C-G
• chr17-38352860-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014598.4(SOCS7):​c.808C>G​(p.Arg270Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000696 in 1,436,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R270W) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: SOCS7 NM_014598.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22336838).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS7	NM_014598.4	c.808C>G	p.Arg270Gly	missense_variant	Exon 1 of 10	ENST00000612932.6	NP_055413.2
SOCS7	XM_017024551.2	c.808C>G	p.Arg270Gly	missense_variant	Exon 1 of 9		XP_016880040.1
SOCS7	XM_017024552.2	c.808C>G	p.Arg270Gly	missense_variant	Exon 1 of 8		XP_016880041.1
SOCS7	XR_007065295.1	n.1017C>G		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS7	ENST00000612932.6	c.808C>G	p.Arg270Gly	missense_variant	Exon 1 of 10	1	NM_014598.4	ENSP00000482229.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.96e-7 AC: 1 AN: 1436000 Hom.: 0 Cov.: 34 AF XY: 0.00000140 AC XY: 1 AN XY: 711892

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000122

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Uncertain	0.040	T
BayesDel_noAF	Benign	-0.18
CADD	Uncertain	25
DANN	Benign	0.95
DEOGEN2	Uncertain	0.61	.;D
Eigen	Uncertain	0.25
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.77	D
M_CAP	Benign	0.052	D
MetaRNN	Benign	0.22	T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.8	.;L
PrimateAI	Pathogenic	0.83	D
Sift4G	Benign	0.33	T;T
Polyphen		0.80	.;P
Vest4		0.28
MutPred		0.23		Loss of methylation at R206 (P = 0.0095);Loss of methylation at R206 (P = 0.0095);
MVP		0.78
ClinPred		0.83	D
GERP RS		4.4
Varity_R		0.24
gMVP		0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-36508743;