13-97866334-A-G

Variant names:

• chr13-97866334-A-G
• rs1337791

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 0.766 in 152,072 control chromosomes in the GnomAD database, including 44,855 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 0.77 (44855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116501 AN: 151954 Hom.: 44836 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.766 AC: 116562 AN: 152072 Hom.: 44855 Cov.: 32 AF XY: 0.763 AC XY: 56721 AN XY: 74316

African (AFR) AF: 0.755 AC: 31316 AN: 41500

American (AMR) AF: 0.702 AC: 10730 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3651 AN: 5148

South Asian (SAS) AF: 0.886 AC: 4267 AN: 4814

European-Finnish (FIN) AF: 0.685 AC: 7235 AN: 10564

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53893 AN: 67982

Other (OTH) AF: 0.764 AC: 1610 AN: 2106

Alfa AF: 0.792 Hom.: 35106

Bravo AF: 0.764

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.62
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1337791; hg19: chr13-98518588;