rs10506458

Variant names:

• chr12-63051312-G-A
• rs10506458

Your query was ambiguous. Multiple possible variants found:

• chr12-63051312-G-A
• chr12-63051312-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 0.0988 in 152,176 control chromosomes in the GnomAD database, including 866 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 0.099 (866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 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: 0.0989 AC: 15033 AN: 152058 Hom.: 866 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0988 AC: 15037 AN: 152176 Hom.: 866 Cov.: 32 AF XY: 0.0996 AC XY: 7412 AN XY: 74392

African (AFR) AF: 0.0487 AC: 2021 AN: 41524

American (AMR) AF: 0.133 AC: 2033 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3472

East Asian (EAS) AF: 0.181 AC: 937 AN: 5182

South Asian (SAS) AF: 0.138 AC: 667 AN: 4828

European-Finnish (FIN) AF: 0.0926 AC: 982 AN: 10602

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7456 AN: 67992

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.0982 Hom.: 969

Bravo AF: 0.102

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.45
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs10506458; hg19: chr12-63445092;