rs1876482

Variant names:

• chr2-17181301-G-A
• rs1876482
• ENST00000845015.1:n.253+12063C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-17181301-G-A
• chr2-17181301-G-C

Variant summary

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

The ENST00000845015.1(ENSG00000309887):​n.253+12063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,244 control chromosomes in the GnomAD database, including 2,115 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 0.091 (2115 hom., cov: 32)
• Consequence: ENSG00000309887 ENST00000845015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 13 publications found

Genes affected

ENSG00000309887 (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 = 0.734 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
ENSG00000309887	ENST00000845015.1	n.253+12063C>T		intron_variant	Intron 1 of 2
ENSG00000309902	ENST00000845391.1	n.216+2104G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13768 AN: 152126 Hom.: 2110 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0905 AC: 13785 AN: 152244 Hom.: 2115 Cov.: 32 AF XY: 0.100 AC XY: 7472 AN XY: 74440

African (AFR) AF: 0.0167 AC: 695 AN: 41564

American (AMR) AF: 0.159 AC: 2437 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3896 AN: 5172

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3840 AN: 68012

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.0774 Hom.: 2522

Bravo AF: 0.0934

Asia WGS AF: 0.456 AC: 1581 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	2.9
DANN	Benign	0.30
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1876482; hg19: chr2-17362568;