rs4347891

chr2-136278108-G-Achr2-136278108-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;