rs2717068

chr2-57867738-A-Cchr2-57867738-A-Gchr2-57867738-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 0.698 in 152,044 control chromosomes in the GnomAD database, including 38,456 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 0.70 (38456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.698 AC: 106015 AN: 151926 Hom.: 38408 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.698 AC: 106121 AN: 152044 Hom.: 38456 Cov.: 31 AF XY: 0.694 AC XY: 51563 AN XY: 74316

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.670

Alfa AF: 0.656 Hom.: 4295

Bravo AF: 0.706

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.3
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2717068; hg19: chr2-58094873;