rs10505975

Variant names:

• chr12-25323285-G-A
• rs10505975

Your query was ambiguous. Multiple possible variants found:

• chr12-25323285-G-A
• chr12-25323285-G-C
• chr12-25323285-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 0.795 in 152,146 control chromosomes in the GnomAD database, including 49,649 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 0.79 (49649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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: 0.795 AC: 120845 AN: 152028 Hom.: 49629 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.795 AC: 120914 AN: 152146 Hom.: 49649 Cov.: 32 AF XY: 0.796 AC XY: 59179 AN XY: 74388

African (AFR) AF: 0.564 AC: 23368 AN: 41456

American (AMR) AF: 0.827 AC: 12653 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3035 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4484 AN: 5176

South Asian (SAS) AF: 0.824 AC: 3973 AN: 4824

European-Finnish (FIN) AF: 0.906 AC: 9599 AN: 10590

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60964 AN: 68016

Other (OTH) AF: 0.809 AC: 1711 AN: 2114

Alfa AF: 0.864 Hom.: 28295

Bravo AF: 0.780

Asia WGS AF: 0.792 AC: 2754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10505975; hg19: chr12-25476219;