chr11-129528916-C-T

Position:

• chr11-129528916-C-T

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 0.275 in 152,138 control chromosomes in the GnomAD database, including 6,077 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 0.28 (6077 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.275 AC: 41845 AN: 152020 Hom.: 6070 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.00461

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.275 AC: 41874 AN: 152138 Hom.: 6077 Cov.: 33 AF XY: 0.270 AC XY: 20045 AN XY: 74368

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.290

Alfa AF: 0.287 Hom.: 13201

Bravo AF: 0.275

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2008849; hg19: chr11-129398811;