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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.931 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

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 0.976

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.946

Alfa AF: 0.941 Hom.: 9839

Bravo AF: 0.926

Asia WGS AF: 0.989 AC: 3427 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2440915; hg19: chr10-61673772;