rs1629422

chr2-140181183-A-Gchr2-140181183-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.431

Alfa AF: 0.390 Hom.: 1970

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1629422; hg19: chr2-140938752;