17-78369710-T-C

Variant names:

• chr17-78369710-T-C
• rs4969172
• ENST00000592569.1:n.640+817T>C

Variant summary

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

The ENST00000592569.1(SOCS3-DT):​n.640+817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,040 control chromosomes in the GnomAD database, including 23,282 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 0.53 (23282 hom., cov: 32)
• Consequence: SOCS3-DT ENST00000592569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS3-DT	NR_110847.1	n.645+817T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.640+817T>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80305 AN: 151922 Hom.: 23289 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.528 AC: 80313 AN: 152040 Hom.: 23282 Cov.: 32 AF XY: 0.529 AC XY: 39273 AN XY: 74306

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.521

Alfa AF: 0.569 Hom.: 6435

Bravo AF: 0.507

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4969172; hg19: chr17-76365791;