chr17-78367559-A-C

Variant names:

• chr17-78367559-A-C
• rs12952093
• ENST00000592569.1:n.474+293A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592569.1(SOCS3-DT):​n.474+293A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,176 control chromosomes in the GnomAD database, including 35,464 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 0.68 (35464 hom., cov: 34)
• Consequence: SOCS3-DT ENST00000592569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 9 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS3-DT	NR_110847.1	n.479+293A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.474+293A>C		intron_variant	Intron 3 of 4	3
SOCS3-DT	ENST00000794147.1	n.660+293A>C		intron_variant	Intron 4 of 4
SOCS3-DT	ENST00000794148.1	n.501+293A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103455 AN: 152058 Hom.: 35442 Cov.: 34

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.680 AC: 103523 AN: 152176 Hom.: 35464 Cov.: 34 AF XY: 0.679 AC XY: 50474 AN XY: 74390

African (AFR) AF: 0.629 AC: 26086 AN: 41498

American (AMR) AF: 0.706 AC: 10796 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2507 AN: 5186

South Asian (SAS) AF: 0.692 AC: 3339 AN: 4826

European-Finnish (FIN) AF: 0.691 AC: 7308 AN: 10578

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48889 AN: 68006

Other (OTH) AF: 0.669 AC: 1415 AN: 2114

Alfa AF: 0.669 Hom.: 6910

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.13
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12952093; hg19: chr17-76363640;