11-54661979-A-G

Variant names:

• chr11-54661979-A-G
• rs492496

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 0.899 in 152,244 control chromosomes in the GnomAD database, including 62,392 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 0.90 (62392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136854 AN: 152126 Hom.: 62361 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.899 AC: 136941 AN: 152244 Hom.: 62392 Cov.: 33 AF XY: 0.902 AC XY: 67164 AN XY: 74432

African (AFR) AF: 0.743 AC: 30827 AN: 41510

American (AMR) AF: 0.957 AC: 14627 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5165 AN: 5168

South Asian (SAS) AF: 0.992 AC: 4785 AN: 4826

European-Finnish (FIN) AF: 0.944 AC: 10029 AN: 10622

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65025 AN: 68036

Other (OTH) AF: 0.923 AC: 1952 AN: 2114

Alfa AF: 0.914 Hom.: 8978

Bravo AF: 0.893

Asia WGS AF: 0.980 AC: 3409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs492496; hg19: chr11-51457301;