rs2440915

Variant names:

• chr10-59914014-G-A
• rs2440915

Your query was ambiguous. Multiple possible variants found:

• chr10-59914014-G-A
• chr10-59914014-G-C
• chr10-59914014-G-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 0.931 in 152,266 control chromosomes in the GnomAD database, including 66,333 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 0.93 (66333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141651 AN: 152148 Hom.: 66283 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.931 AC: 141759 AN: 152266 Hom.: 66333 Cov.: 32 AF XY: 0.934 AC XY: 69576 AN XY: 74460

African (AFR) AF: 0.825 AC: 34267 AN: 41522

American (AMR) AF: 0.966 AC: 14786 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3430 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5174

South Asian (SAS) AF: 0.993 AC: 4791 AN: 4826

European-Finnish (FIN) AF: 0.976 AC: 10360 AN: 10614

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65773 AN: 68038

Other (OTH) AF: 0.946 AC: 2002 AN: 2116

Alfa AF: 0.952 Hom.: 18436

Bravo AF: 0.926

Asia WGS AF: 0.989 AC: 3427 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.67
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2440915; hg19: chr10-61673772;