rs2405657

Variant names:

• chr11-97811564-A-G
• rs2405657

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 0.654 in 151,990 control chromosomes in the GnomAD database, including 33,033 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 0.65 (33033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.654 AC: 99342 AN: 151872 Hom.: 32992 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.654 AC: 99439 AN: 151990 Hom.: 33033 Cov.: 32 AF XY: 0.648 AC XY: 48104 AN XY: 74264

African (AFR) AF: 0.739 AC: 30655 AN: 41474

American (AMR) AF: 0.603 AC: 9204 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2351 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2141 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2744 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6016 AN: 10540

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44252 AN: 67936

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

Alfa AF: 0.645 Hom.: 115388

Bravo AF: 0.655

Asia WGS AF: 0.518 AC: 1801 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2405657; hg19: chr11-97682564;