11-102849613-T-A

Position:

• chr11-102849613-T-A

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 0.0932 in 152,242 control chromosomes in the GnomAD database, including 939 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 0.093 (939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.0932 AC: 14184 AN: 152124 Hom.: 938 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.0932 AC: 14186 AN: 152242 Hom.: 939 Cov.: 32 AF XY: 0.0946 AC XY: 7041 AN XY: 74428

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.0709

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0261

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0896

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.0799

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17361668; hg19: chr11-102720344;