chr11-130477295-G-T

Position:

• chr11-130477295-G-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 0.384 in 152,044 control chromosomes in the GnomAD database, including 11,807 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 0.38 (11807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.384 AC: 58333 AN: 151926 Hom.: 11787 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.384 AC: 58402 AN: 152044 Hom.: 11807 Cov.: 32 AF XY: 0.387 AC XY: 28749 AN XY: 74300

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.386

Alfa AF: 0.328 Hom.: 17298

Bravo AF: 0.389

Asia WGS AF: 0.451 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4937523; hg19: chr11-130347190;