11-2999510-C-T

Variant names:

• chr11-2999510-C-T
• rs12805661

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 0.259 in 152,082 control chromosomes in the GnomAD database, including 6,716 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 0.26 (6716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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 = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39337 AN: 151964 Hom.: 6704 Cov.: 32

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.259 AC: 39358 AN: 152082 Hom.: 6716 Cov.: 32 AF XY: 0.263 AC XY: 19532 AN XY: 74318

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.298

Alfa AF: 0.169 Hom.: 383

Bravo AF: 0.267

Asia WGS AF: 0.495 AC: 1718 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	0.64
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12805661; hg19: chr11-3020740;