chr11-92988153-G-A

Variant names:

• chr11-92988153-G-A
• rs1597023

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 0.558 in 151,784 control chromosomes in the GnomAD database, including 23,933 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 0.56 (23933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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: 0.558 AC: 84573 AN: 151664 Hom.: 23901 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.558 AC: 84668 AN: 151784 Hom.: 23933 Cov.: 31 AF XY: 0.566 AC XY: 41997 AN XY: 74178

African (AFR) AF: 0.560 AC: 23173 AN: 41364

American (AMR) AF: 0.658 AC: 10039 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1520 AN: 3460

East Asian (EAS) AF: 0.694 AC: 3584 AN: 5162

South Asian (SAS) AF: 0.688 AC: 3311 AN: 4810

European-Finnish (FIN) AF: 0.576 AC: 6054 AN: 10514

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35051 AN: 67904

Other (OTH) AF: 0.542 AC: 1146 AN: 2114

Alfa AF: 0.533 Hom.: 11337

Bravo AF: 0.564

Asia WGS AF: 0.649 AC: 2253 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.94
DANN	Benign	0.69
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1597023; hg19: chr11-92721319;