rs1522653

Variant names:

• chr11-81141153-T-C
• rs1522653

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 0.0658 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0659 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

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0599 Hom.: 148

Bravo AF: 0.0599

Asia WGS AF: 0.165 AC: 572 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1522653; hg19: chr11-80852196;