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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739888.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296490	ENST00000739888.1		n.586+1335A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1629422;

hg19: chr2-140938752;