chr10-113970971-A-G

Variant names:

• chr10-113970971-A-G
• rs180934

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 0.569 in 152,132 control chromosomes in the GnomAD database, including 25,661 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 0.57 (25661 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 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: 0.569 AC: 86503 AN: 152014 Hom.: 25643 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.569 AC: 86566 AN: 152132 Hom.: 25661 Cov.: 33 AF XY: 0.578 AC XY: 42998 AN XY: 74392

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.543

Alfa AF: 0.595 Hom.: 4560

Bravo AF: 0.548

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180934; hg19: chr10-115730730;