rs10111661

chr8-20479062-G-A

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 0.398 in 152,106 control chromosomes in the GnomAD database, including 12,636 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 0.40 (12636 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.398 AC: 60489 AN: 151988 Hom.: 12632 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.398 AC: 60532 AN: 152106 Hom.: 12636 Cov.: 33 AF XY: 0.405 AC XY: 30144 AN XY: 74342

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.418

Alfa AF: 0.403 Hom.: 5960

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.7
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10111661; hg19: chr8-20336573;