chr11-13217783-A-G

Position:

• chr11-13217783-A-G

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 0.235 in 152,098 control chromosomes in the GnomAD database, including 4,505 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 0.23 (4505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.235 AC: 35726 AN: 151980 Hom.: 4505 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.235 AC: 35728 AN: 152098 Hom.: 4505 Cov.: 32 AF XY: 0.234 AC XY: 17365 AN XY: 74358

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.199

Alfa AF: 0.241 Hom.: 9312

Bravo AF: 0.235

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11022713; hg19: chr11-13239330;