rs1528753

Positions:

• chr11-91151171-A-C

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 0.7 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91151171A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.731

Alfa AF: 0.770 Hom.: 96992

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1528753; hg19: chr11-90884339;