rs693092

Positions:

• chr13-88407900-G-A

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 0.344 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.316

Alfa AF: 0.356 Hom.: 10482

Bravo AF: 0.344

Asia WGS AF: 0.419 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs693092; hg19: chr13-89060155;