rs180935

Variant names:

• chr10-113970500-G-A
• rs180935

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 0.533 in 152,058 control chromosomes in the GnomAD database, including 23,402 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 0.53 (23402 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.533 AC: 80947 AN: 151940 Hom.: 23390 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.533 AC: 81000 AN: 152058 Hom.: 23402 Cov.: 33 AF XY: 0.542 AC XY: 40255 AN XY: 74332

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.516

Alfa AF: 0.594 Hom.: 13729

Bravo AF: 0.509

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
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: rs180935; hg19: chr10-115730259;