10-46056060-C-A

Variant names:

• chr10-46056060-C-A
• rs10763588

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 0.454 in 151,962 control chromosomes in the GnomAD database, including 17,380 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 0.45 (17380 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.455 AC: 69072 AN: 151844 Hom.: 17387 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.454 AC: 69064 AN: 151962 Hom.: 17380 Cov.: 31 AF XY: 0.456 AC XY: 33878 AN XY: 74270

African (AFR) AF: 0.227 AC: 9404 AN: 41434

American (AMR) AF: 0.541 AC: 8261 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2643 AN: 5158

South Asian (SAS) AF: 0.412 AC: 1982 AN: 4816

European-Finnish (FIN) AF: 0.611 AC: 6433 AN: 10536

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37267 AN: 67958

Other (OTH) AF: 0.456 AC: 964 AN: 2116

Alfa AF: 0.512 Hom.: 42957

Bravo AF: 0.445

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.86
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10763588; hg19: chr10-51539762;