rs4954391

Positions:

• chr2-136126253-C-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 0.712 in 152,178 control chromosomes in the GnomAD database, including 39,879 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 0.71 (39879 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108298 AN: 152060 Hom.: 39872 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.712 AC: 108347 AN: 152178 Hom.: 39879 Cov.: 33 AF XY: 0.719 AC XY: 53477 AN XY: 74418

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.744

Alfa AF: 0.763 Hom.: 58587

Bravo AF: 0.694

Asia WGS AF: 0.826 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954391; hg19: chr2-136883823; COSMIC: COSV53891189;