rs4954808

Variant names:

• chr2-139942390-T-A
• rs4954808

Your query was ambiguous. Multiple possible variants found:

• chr2-139942390-T-A
• chr2-139942390-T-C
• chr2-139942390-T-G

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 0.672 in 151,924 control chromosomes in the GnomAD database, including 34,449 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 0.67 (34449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.671 AC: 101920 AN: 151804 Hom.: 34404 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.672 AC: 102020 AN: 151924 Hom.: 34449 Cov.: 31 AF XY: 0.679 AC XY: 50435 AN XY: 74262

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.680

Alfa AF: 0.661 Hom.: 4155

Bravo AF: 0.672

Asia WGS AF: 0.750 AC: 2594 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954808; hg19: chr2-140699959;