rs180925

Variant names:

• chr10-113975176-A-C
• rs180925

Your query was ambiguous. Multiple possible variants found:

• chr10-113975176-A-C
• chr10-113975176-A-G
• chr10-113975176-A-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 0.747 in 151,772 control chromosomes in the GnomAD database, including 42,611 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 0.75 (42611 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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: 0.747 AC: 113289 AN: 151652 Hom.: 42559 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.747 AC: 113404 AN: 151772 Hom.: 42611 Cov.: 30 AF XY: 0.753 AC XY: 55840 AN XY: 74164

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.695

Alfa AF: 0.721 Hom.: 37895

Bravo AF: 0.734

Asia WGS AF: 0.674 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180925; hg19: chr10-115734935;