rs697651

Variant names:

• chr2-154466766-C-A
• rs697651

Your query was ambiguous. Multiple possible variants found:

• chr2-154466766-C-A
• chr2-154466766-C-G
• chr2-154466766-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.549 AC: 22710 AN: 41384

American (AMR) AF: 0.729 AC: 11110 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2288 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2686 AN: 5104

South Asian (SAS) AF: 0.714 AC: 3440 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7184 AN: 10558

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44534 AN: 67890

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.649 Hom.: 49325

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs697651; hg19: chr2-155323278;