10-52823673-A-T

Variant names:

• chr10-52823673-A-T
• rs11819131

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 0.244 in 151,938 control chromosomes in the GnomAD database, including 4,644 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 0.24 (4644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 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: 0.244 AC: 37022 AN: 151820 Hom.: 4636 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.244 AC: 37046 AN: 151938 Hom.: 4644 Cov.: 32 AF XY: 0.244 AC XY: 18106 AN XY: 74288

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.250

Alfa AF: 0.234 Hom.: 524

Bravo AF: 0.256

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11819131; hg19: chr10-54583433;