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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.438 AC: 18177 AN: 41456

American (AMR) AF: 0.655 AC: 10002 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3466

East Asian (EAS) AF: 0.686 AC: 3531 AN: 5148

South Asian (SAS) AF: 0.638 AC: 3064 AN: 4806

European-Finnish (FIN) AF: 0.596 AC: 6289 AN: 10558

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.568 AC: 38600 AN: 67932

Other (OTH) AF: 0.550 AC: 1161 AN: 2112

Alfa AF: 0.555 Hom.: 12281

Bravo AF: 0.548

Asia WGS AF: 0.660 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.63
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs895401; hg19: chr2-119867708;