rs10501805

chr11-93658788-T-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 0.046 in 152,290 control chromosomes in the GnomAD database, including 375 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 0.046 (375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.0459 AC: 6989 AN: 152172 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00885

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0460 AC: 7004 AN: 152290 Hom.: 375 Cov.: 32 AF XY: 0.0451 AC XY: 3357 AN XY: 74466

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00885

Gnomad4 OTH AF: 0.0555

Alfa AF: 0.0300 Hom.: 36

Bravo AF: 0.0533

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501805; hg19: chr11-93391954;