ENST00000592569.1:n.401-384C>T

Variant names:

• chr17-78366809-C-T
• rs9914220
• ENST00000592569.1:n.401-384C>T

Variant summary

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

The ENST00000592569.1(SOCS3-DT):​n.401-384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,270 control chromosomes in the GnomAD database, including 2,574 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 0.15 (2574 hom., cov: 33)
• Consequence: SOCS3-DT ENST00000592569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 18 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592569.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	NR_110847.1		n.406-384C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	ENST00000592569.1	TSL:3	n.401-384C>T		intron	N/A
	SOCS3-DT	ENST00000794147.1		n.587-384C>T		intron	N/A
	SOCS3-DT	ENST00000794148.1		n.428-384C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22208 AN: 152152 Hom.: 2566 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.146 AC: 22251 AN: 152270 Hom.: 2574 Cov.: 33 AF XY: 0.144 AC XY: 10734 AN XY: 74444

African (AFR) AF: 0.296 AC: 12276 AN: 41538

American (AMR) AF: 0.126 AC: 1933 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1998 AN: 5172

South Asian (SAS) AF: 0.154 AC: 744 AN: 4828

European-Finnish (FIN) AF: 0.0209 AC: 222 AN: 10624

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4235 AN: 68022

Other (OTH) AF: 0.145 AC: 307 AN: 2116

Alfa AF: 0.0853 Hom.: 1567

Bravo AF: 0.164

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9914220; hg19: chr17-76362890;