rs697651

chr2-154466766-C-Achr2-154466766-C-Gchr2-154466766-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 0.633 in 151,768 control chromosomes in the GnomAD database, including 30,755 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 0.63 (30755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.718 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: 0.633 AC: 96044 AN: 151650 Hom.: 30730 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.633 AC: 96105 AN: 151768 Hom.: 30755 Cov.: 32 AF XY: 0.637 AC XY: 47227 AN XY: 74150

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.644

Alfa AF: 0.649 Hom.: 40940

Bravo AF: 0.631

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs697651; hg19: chr2-155323278;