rs180925

chr10-113975176-A-Cchr10-113975176-A-Gchr10-113975176-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;