13-97866334-A-G

Variant names:

• chr13-97866334-A-G
• rs1337791

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 0.766 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.767 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

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.764

Alfa AF: 0.795 Hom.: 24779

Bravo AF: 0.764

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1337791; hg19: chr13-98518588;