rs1528753

Variant names:

• chr11-91151171-A-C
• rs1528753

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 0.7 in 151,928 control chromosomes in the GnomAD database, including 38,692 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 0.70 (38692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 8 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 (SAS) allele frequency at 95% confidence interval = 0.792 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: 0.700 AC: 106282 AN: 151808 Hom.: 38692 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.700 AC: 106321 AN: 151928 Hom.: 38692 Cov.: 32 AF XY: 0.704 AC XY: 52292 AN XY: 74232

African (AFR) AF: 0.482 AC: 19958 AN: 41414

American (AMR) AF: 0.766 AC: 11686 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2833 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3456 AN: 5142

South Asian (SAS) AF: 0.813 AC: 3912 AN: 4812

European-Finnish (FIN) AF: 0.814 AC: 8601 AN: 10566

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53367 AN: 67958

Other (OTH) AF: 0.731 AC: 1540 AN: 2108

Alfa AF: 0.753 Hom.: 142221

Bravo AF: 0.685

Asia WGS AF: 0.734 AC: 2550 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.49
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1528753; hg19: chr11-90884339;