rs2962896

Variant names:

• chr5-18417974-A-G
• rs2962896
• ENST00000749495.1:n.204-595A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-18417974-A-G
• chr5-18417974-A-T

Variant summary

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

The ENST00000749495.1(ENSG00000297632):​n.204-595A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,902 control chromosomes in the GnomAD database, including 27,013 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 0.59 (27013 hom., cov: 31)
• Consequence: ENSG00000297632 ENST00000749495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 1 publications found

Genes affected

ENSG00000297632 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 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
ENSG00000297632	ENST00000749495.1	n.204-595A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89340 AN: 151782 Hom.: 27030 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.588 AC: 89342 AN: 151902 Hom.: 27013 Cov.: 31 AF XY: 0.591 AC XY: 43851 AN XY: 74222

African (AFR) AF: 0.478 AC: 19772 AN: 41404

American (AMR) AF: 0.484 AC: 7385 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2341 AN: 3464

East Asian (EAS) AF: 0.523 AC: 2695 AN: 5154

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4816

European-Finnish (FIN) AF: 0.751 AC: 7932 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44338 AN: 67944

Other (OTH) AF: 0.624 AC: 1314 AN: 2106

Alfa AF: 0.626 Hom.: 102849

Bravo AF: 0.564

Asia WGS AF: 0.516 AC: 1793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2962896; hg19: chr5-18418083;