rs2509897

Variant names:

• chr11-57595144-C-G
• rs2509897

Your query was ambiguous. Multiple possible variants found:

• chr11-57595144-C-G
• chr11-57595144-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 0.723 in 152,070 control chromosomes in the GnomAD database, including 40,660 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 0.72 (40660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.722 AC: 109780 AN: 151952 Hom.: 40604 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.723 AC: 109895 AN: 152070 Hom.: 40660 Cov.: 31 AF XY: 0.727 AC XY: 54007 AN XY: 74320

African (AFR) AF: 0.876 AC: 36357 AN: 41494

American (AMR) AF: 0.709 AC: 10823 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2645 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4456 AN: 5184

South Asian (SAS) AF: 0.675 AC: 3250 AN: 4818

European-Finnish (FIN) AF: 0.700 AC: 7392 AN: 10558

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42529 AN: 67966

Other (OTH) AF: 0.709 AC: 1498 AN: 2112

Alfa AF: 0.573 Hom.: 1613

Bravo AF: 0.731

Asia WGS AF: 0.770 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.63
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2509897; hg19: chr11-57362617;