rs2947411

chr2-614168-A-Gchr2-614168-A-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 0.816 in 152,092 control chromosomes in the GnomAD database, including 50,719 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 0.82 (50719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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: 0.816 AC: 123981 AN: 151972 Hom.: 50696 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.792

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.816 AC: 124055 AN: 152092 Hom.: 50719 Cov.: 31 AF XY: 0.819 AC XY: 60858 AN XY: 74334

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.813

Alfa AF: 0.823 Hom.: 58147

Bravo AF: 0.815

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2947411; hg19: chr2-614168;