chr11-13275014-T-C

Position:

• chr11-13275014-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 0.25 in 152,020 control chromosomes in the GnomAD database, including 5,109 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 0.25 (5109 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.250 AC: 38013 AN: 151902 Hom.: 5111 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.250 AC: 38005 AN: 152020 Hom.: 5109 Cov.: 31 AF XY: 0.252 AC XY: 18706 AN XY: 74312

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.233

Alfa AF: 0.252 Hom.: 3961

Bravo AF: 0.246

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11022742; hg19: chr11-13296561;