11-91554359-T-C

Variant names:

• chr11-91554359-T-C
• rs2514299

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 0.591 in 151,958 control chromosomes in the GnomAD database, including 27,135 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 0.59 (27135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89783 AN: 151838 Hom.: 27100 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.591 AC: 89878 AN: 151958 Hom.: 27135 Cov.: 32 AF XY: 0.595 AC XY: 44171 AN XY: 74264

African (AFR) AF: 0.667 AC: 27640 AN: 41428

American (AMR) AF: 0.656 AC: 10015 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4160 AN: 5150

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4818

European-Finnish (FIN) AF: 0.641 AC: 6761 AN: 10544

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35504 AN: 67958

Other (OTH) AF: 0.591 AC: 1248 AN: 2112

Alfa AF: 0.540 Hom.: 92375

Bravo AF: 0.599

Asia WGS AF: 0.613 AC: 2130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2514299; hg19: chr11-91287525;