rs4994934

chr17-78368596-T-C

Variant summary

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

The NR_110847.1(SOCS3-DT):n.480-132T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,348 control chromosomes in the GnomAD database, including 62,870 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 0.91 (62814 hom., cov: 33)
  • Exomes 𝑓: 0.88 (56 hom.)
• Consequence: SOCS3-DT NR_110847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOCS3-DT	NR_110847.1	n.480-132T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.475-132T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138039 AN: 152086 Hom.: 62770 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.903

GnomAD4 exome AF: 0.882 AC: 127 AN: 144 Hom.: 56 AF XY: 0.914 AC XY: 106 AN XY: 116

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.908

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.908 AC: 138142 AN: 152204 Hom.: 62814 Cov.: 33 AF XY: 0.908 AC XY: 67545 AN XY: 74396

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.903

Alfa AF: 0.907 Hom.: 7764

Bravo AF: 0.904

Asia WGS AF: 0.863 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.3
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4994934; hg19: chr17-76364677;