rs1528767

Variant names:

• chr11-91006382-T-C
• rs1528767

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 0.23 in 152,078 control chromosomes in the GnomAD database, including 4,996 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 0.23 (4996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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: 0.230 AC: 34983 AN: 151958 Hom.: 4993 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.230 AC: 34987 AN: 152078 Hom.: 4996 Cov.: 32 AF XY: 0.228 AC XY: 16917 AN XY: 74328

African (AFR) AF: 0.0653 AC: 2713 AN: 41526

American (AMR) AF: 0.204 AC: 3112 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1041 AN: 3464

East Asian (EAS) AF: 0.104 AC: 536 AN: 5154

South Asian (SAS) AF: 0.238 AC: 1150 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3018 AN: 10550

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22568 AN: 67974

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.305 Hom.: 10582

Bravo AF: 0.217

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.43
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1528767; hg19: chr11-90739550;