17-78363490-T-C

Variant names:

• chr17-78363490-T-C
• rs12949584
• ENST00000587575.1:n.81+739T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587575.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	NR_110845.1		n.461+739T>C		intron	N/A
	SOCS3-DT	NR_110846.1		n.138+739T>C		intron	N/A
	SOCS3-DT	NR_110847.1		n.405+739T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	ENST00000587575.1	TSL:3	n.81+739T>C		intron	N/A
	SOCS3-DT	ENST00000592569.1	TSL:3	n.400+739T>C		intron	N/A
	SOCS3-DT	ENST00000687996.3		n.489+739T>C		intron	N/A

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

African (AFR) AF: 0.941 AC: 39014 AN: 41470

American (AMR) AF: 0.896 AC: 13694 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3088 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3426 AN: 5158

South Asian (SAS) AF: 0.943 AC: 4538 AN: 4812

European-Finnish (FIN) AF: 0.899 AC: 9501 AN: 10570

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62392 AN: 67958

Other (OTH) AF: 0.901 AC: 1899 AN: 2108

Alfa AF: 0.911 Hom.: 7675

Bravo AF: 0.908

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12949584;

hg19: chr17-76359571;