rs693092

Variant names:

• chr13-88407900-G-A
• rs693092

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 0.344 in 151,888 control chromosomes in the GnomAD database, including 9,476 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 0.34 (9476 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52202 AN: 151770 Hom.: 9459 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.344 AC: 52253 AN: 151888 Hom.: 9476 Cov.: 31 AF XY: 0.352 AC XY: 26099 AN XY: 74210

African (AFR) AF: 0.244 AC: 10105 AN: 41462

American (AMR) AF: 0.458 AC: 6980 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1102 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2493 AN: 5132

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4808

European-Finnish (FIN) AF: 0.456 AC: 4803 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24182 AN: 67928

Other (OTH) AF: 0.316 AC: 664 AN: 2104

Alfa AF: 0.353 Hom.: 13383

Bravo AF: 0.344

Asia WGS AF: 0.419 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs693092; hg19: chr13-89060155;