10-113970971-A-G

Position:

• chr10-113970971-A-G

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/exons	MANE	UniProt

Ensembl

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