rs13013484

chr2-27765954-G-A

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 0.614 in 152,100 control chromosomes in the GnomAD database, including 30,137 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 0.61 (30137 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977

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 = 0.727 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: 0.615 AC: 93426 AN: 151980 Hom.: 30143 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.614 AC: 93435 AN: 152100 Hom.: 30137 Cov.: 33 AF XY: 0.609 AC XY: 45302 AN XY: 74348

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.645

Alfa AF: 0.710 Hom.: 78556

Bravo AF: 0.591

Asia WGS AF: 0.516 AC: 1796 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	7.1
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13013484; hg19: chr2-27988821;