11-54825685-C-T

Variant names:

• chr11-54825685-C-T
• rs1580785

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.679 in 151,472 control chromosomes in the GnomAD database, including 35,508 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 0.68 (35508 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.761 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: 0.679 AC: 102783 AN: 151354 Hom.: 35485 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.679 AC: 102848 AN: 151472 Hom.: 35508 Cov.: 33 AF XY: 0.678 AC XY: 50206 AN XY: 73998

African (AFR) AF: 0.564 AC: 23306 AN: 41358

American (AMR) AF: 0.772 AC: 11692 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2772 AN: 3466

East Asian (EAS) AF: 0.768 AC: 3967 AN: 5168

South Asian (SAS) AF: 0.771 AC: 3720 AN: 4826

European-Finnish (FIN) AF: 0.658 AC: 6952 AN: 10560

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48072 AN: 67658

Other (OTH) AF: 0.717 AC: 1501 AN: 2092

Alfa AF: 0.714 Hom.: 34525

Bravo AF: 0.682

Asia WGS AF: 0.769 AC: 2674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.58

Splicing

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

Other links and lift over

dbSNP: rs1580785; hg19: chr11-51293595;