rs10892301

chr11-118864767-G-Achr11-118864767-G-T

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 0.399 in 151,916 control chromosomes in the GnomAD database, including 12,499 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 (12499 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.400 AC: 60659 AN: 151796 Hom.: 12503 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.399 AC: 60658 AN: 151916 Hom.: 12499 Cov.: 31 AF XY: 0.403 AC XY: 29893 AN XY: 74252

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.411

Alfa AF: 0.422 Hom.: 27538

Bravo AF: 0.380

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10892301; hg19: chr11-118735476;