ENST00000700856.2:n.889C>A

Variant names:

• chr17-78361310-C-A
• rs8064821
• ENST00000700856.2:n.889C>A

Variant summary

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

The ENST00000700856.2(SOCS3-DT):​n.889C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,066 control chromosomes in the GnomAD database, including 2,516 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 0.17 (2516 hom., cov: 32)
• Consequence: SOCS3-DT ENST00000700856.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 22 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOCS3-DT	NR_110845.1	n.327-456C>A		intron_variant	Intron 1 of 3
SOCS3-DT	NR_110846.1	n.59+250C>A		intron_variant	Intron 1 of 2
SOCS3-DT	NR_110847.1	n.326+537C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS3-DT	ENST00000700856.2	n.889C>A		non_coding_transcript_exon_variant	Exon 1 of 1
SOCS3-DT	ENST00000794189.1	n.863C>A		non_coding_transcript_exon_variant	Exon 1 of 2
SOCS3-DT	ENST00000592569.1	n.321+537C>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25526 AN: 151946 Hom.: 2511 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 25559 AN: 152066 Hom.: 2516 Cov.: 32 AF XY: 0.169 AC XY: 12597 AN XY: 74330

African (AFR) AF: 0.273 AC: 11327 AN: 41454

American (AMR) AF: 0.122 AC: 1868 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1190 AN: 5154

South Asian (SAS) AF: 0.168 AC: 811 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7968 AN: 67964

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.158 Hom.: 2007

Bravo AF: 0.170

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.94
DANN	Benign	0.82
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8064821; hg19: chr17-76357391;