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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.809

Alfa AF: 0.865 Hom.: 25138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505975; hg19: chr12-25476219;