rs1877563

Variant names:

• chr3-39262973-G-A
• rs1877563
• ENST00000656239.1:n.2475G>A

Variant summary

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

The ENST00000656239.1(ENSG00000287958):​n.2475G>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 0.117 in 152,216 control chromosomes in the GnomAD database, including 1,101 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 0.12 (1101 hom., cov: 32)
• Consequence: ENSG00000287958 ENST00000656239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 9 publications found

Genes affected

ENSG00000287958 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287958	ENST00000656239.1	n.2475G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17856 AN: 152098 Hom.: 1100 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.117 AC: 17862 AN: 152216 Hom.: 1101 Cov.: 32 AF XY: 0.118 AC XY: 8787 AN XY: 74414

African (AFR) AF: 0.140 AC: 5816 AN: 41514

American (AMR) AF: 0.0712 AC: 1089 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5174

South Asian (SAS) AF: 0.121 AC: 582 AN: 4828

European-Finnish (FIN) AF: 0.125 AC: 1319 AN: 10590

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7289 AN: 68016

Other (OTH) AF: 0.0978 AC: 207 AN: 2116

Alfa AF: 0.110 Hom.: 762

Bravo AF: 0.117

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.80
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1877563; hg19: chr3-39304464;