13-88098191-A-G

Variant names:

• chr13-88098191-A-G
• rs1333798

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 0.85 in 151,858 control chromosomes in the GnomAD database, including 54,946 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 0.85 (54946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.850 AC: 129010 AN: 151740 Hom.: 54899 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.850 AC: 129109 AN: 151858 Hom.: 54946 Cov.: 32 AF XY: 0.851 AC XY: 63140 AN XY: 74208

African (AFR) AF: 0.859 AC: 35639 AN: 41480

American (AMR) AF: 0.880 AC: 13382 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3046 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4800 AN: 5162

South Asian (SAS) AF: 0.887 AC: 4279 AN: 4822

European-Finnish (FIN) AF: 0.816 AC: 8636 AN: 10584

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56537 AN: 67818

Other (OTH) AF: 0.876 AC: 1844 AN: 2104

Alfa AF: 0.842 Hom.: 69648

Bravo AF: 0.855

Asia WGS AF: 0.930 AC: 3232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs1333798; hg19: chr13-88750446; COSMIC: COSV60062189;