rs4347891

Variant names:

• chr2-136278108-G-A
• rs4347891

Your query was ambiguous. Multiple possible variants found:

• chr2-136278108-G-A
• chr2-136278108-G-C

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 0.835 in 152,166 control chromosomes in the GnomAD database, including 54,487 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 0.84 (54487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.836 AC: 127072 AN: 152048 Hom.: 54476 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.835 AC: 127114 AN: 152166 Hom.: 54487 Cov.: 32 AF XY: 0.835 AC XY: 62081 AN XY: 74382

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.838

Alfa AF: 0.890 Hom.: 12669

Bravo AF: 0.813

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4347891; hg19: chr2-137035678;