17-78363490-T-C

Position:

• chr17-78363490-T-C

Variant summary

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

The ENST00000587575.1(SOCS3-DT):​n.81+739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,028 control chromosomes in the GnomAD database, including 63,473 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 (63473 hom., cov: 29)
• Consequence: SOCS3-DT ENST00000587575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

SOCS3-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOCS3-DT	NR_110845.1	n.461+739T>C		intron_variant
SOCS3-DT	NR_110846.1	n.138+739T>C		intron_variant
SOCS3-DT	NR_110847.1	n.405+739T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOCS3-DT	ENST00000587575.1	n.81+739T>C		intron_variant		3
SOCS3-DT	ENST00000592569.1	n.400+739T>C		intron_variant		3
SOCS3-DT	ENST00000687996.2	n.477+739T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138567 AN: 151910 Hom.: 63426 Cov.: 29

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.912 AC: 138672 AN: 152028 Hom.: 63473 Cov.: 29 AF XY: 0.911 AC XY: 67680 AN XY: 74294

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.901

Alfa AF: 0.909 Hom.: 7326

Bravo AF: 0.908

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12949584; hg19: chr17-76359571;