chr11-91924110-T-C

Position:

• chr11-91924110-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.149 in 152,186 control chromosomes in the GnomAD database, including 1,967 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 0.15 (1967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22712 AN: 152068 Hom.: 1971 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.149 AC: 22709 AN: 152186 Hom.: 1967 Cov.: 32 AF XY: 0.149 AC XY: 11104 AN XY: 74404

Gnomad4 AFR AF: 0.0771

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.151

Alfa AF: 0.182 Hom.: 2373

Bravo AF: 0.139

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501765; hg19: chr11-91657276;