rs895401

Variant names:

• chr2-119110132-G-A
• rs895401

Your query was ambiguous. Multiple possible variants found:

• chr2-119110132-G-A
• chr2-119110132-G-C
• chr2-119110132-G-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 0.549 in 151,944 control chromosomes in the GnomAD database, including 23,378 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 0.55 (23378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83347 AN: 151826 Hom.: 23359 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.549 AC: 83402 AN: 151944 Hom.: 23378 Cov.: 32 AF XY: 0.554 AC XY: 41111 AN XY: 74262

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.550

Alfa AF: 0.555 Hom.: 10973

Bravo AF: 0.548

Asia WGS AF: 0.660 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs895401; hg19: chr2-119867708;