11-76840204-G-C

Variant names:

• chr11-76840204-G-C
• rs1225130

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 0.561 in 152,032 control chromosomes in the GnomAD database, including 25,498 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 0.56 (25498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.561 AC: 85164 AN: 151914 Hom.: 25461 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.561 AC: 85251 AN: 152032 Hom.: 25498 Cov.: 32 AF XY: 0.565 AC XY: 41984 AN XY: 74286

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.555

Alfa AF: 0.527 Hom.: 2067

Bravo AF: 0.574

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1225130; hg19: chr11-76551248;