rs1522653

Variant names:

• chr11-81141153-T-C
• rs1522653

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 0.0658 in 151,910 control chromosomes in the GnomAD database, including 464 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 0.066 (464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 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 = 0.228 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: 0.0659 AC: 9996 AN: 151792 Hom.: 463 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0658 AC: 9989 AN: 151910 Hom.: 464 Cov.: 32 AF XY: 0.0701 AC XY: 5207 AN XY: 74230

African (AFR) AF: 0.0495 AC: 2058 AN: 41536

American (AMR) AF: 0.0494 AC: 752 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3464

East Asian (EAS) AF: 0.239 AC: 1229 AN: 5134

South Asian (SAS) AF: 0.124 AC: 598 AN: 4824

European-Finnish (FIN) AF: 0.117 AC: 1244 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3754 AN: 67824

Other (OTH) AF: 0.0540 AC: 114 AN: 2110

Alfa AF: 0.0596 Hom.: 161

Bravo AF: 0.0599

Asia WGS AF: 0.165 AC: 572 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.53
PhyloP100		0.073

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1522653;

hg19: chr11-80852196;