rs1629422

Variant names:

• chr2-140181183-A-G
• rs1629422
• ENST00000739888.1:n.586+1335A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-140181183-A-G
• chr2-140181183-A-T

Variant summary

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

The ENST00000739888.1(ENSG00000296490):​n.586+1335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,860 control chromosomes in the GnomAD database, including 15,929 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 0.44 (15929 hom., cov: 32)
• Consequence: ENSG00000296490 ENST00000739888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• Publications: 3 publications found

Genes affected

ENSG00000296490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985822	XR_001739215.1	n.*63A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296490	ENST00000739888.1	n.586+1335A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66096 AN: 151742 Hom.: 15904 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.436 AC: 66179 AN: 151860 Hom.: 15929 Cov.: 32 AF XY: 0.436 AC XY: 32363 AN XY: 74216

African (AFR) AF: 0.638 AC: 26404 AN: 41416

American (AMR) AF: 0.499 AC: 7614 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2324 AN: 5132

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3122 AN: 10522

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21864 AN: 67938

Other (OTH) AF: 0.431 AC: 908 AN: 2108

Alfa AF: 0.398 Hom.: 2137

Bravo AF: 0.457

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1629422; hg19: chr2-140938752;