rs11018023

chr10-131531763-G-Achr10-131531763-G-C

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 0.183 in 152,066 control chromosomes in the GnomAD database, including 2,978 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 0.18 (2978 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 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: 0.183 AC: 27858 AN: 151948 Hom.: 2974 Cov.: 34

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.183 AC: 27872 AN: 152066 Hom.: 2978 Cov.: 34 AF XY: 0.181 AC XY: 13463 AN XY: 74334

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.163

Alfa AF: 0.210 Hom.: 2463

Bravo AF: 0.186

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11018023; hg19: chr10-133330026;