rs10465895

Variant names:

• chr1-24150221-T-A
• rs10465895

Your query was ambiguous. Multiple possible variants found:

• chr1-24150221-T-A
• chr1-24150221-T-C

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 0.842 in 152,214 control chromosomes in the GnomAD database, including 54,432 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 0.84 (54432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.842 AC: 128044 AN: 152096 Hom.: 54386 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.842 AC: 128142 AN: 152214 Hom.: 54432 Cov.: 32 AF XY: 0.846 AC XY: 62930 AN XY: 74416

African (AFR) AF: 0.723 AC: 30022 AN: 41518

American (AMR) AF: 0.896 AC: 13710 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5172

South Asian (SAS) AF: 0.859 AC: 4144 AN: 4826

European-Finnish (FIN) AF: 0.931 AC: 9868 AN: 10604

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59522 AN: 68004

Other (OTH) AF: 0.854 AC: 1801 AN: 2108

Alfa AF: 0.847 Hom.: 2805

Bravo AF: 0.835

Asia WGS AF: 0.912 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10465895; hg19: chr1-24476711;