chr13-88363678-G-A

Variant names:

• chr13-88363678-G-A
• rs1335485

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 0.716 in 151,938 control chromosomes in the GnomAD database, including 39,226 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 0.72 (39226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.786 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: 0.717 AC: 108796 AN: 151822 Hom.: 39209 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.716 AC: 108859 AN: 151938 Hom.: 39226 Cov.: 31 AF XY: 0.715 AC XY: 53052 AN XY: 74246

African (AFR) AF: 0.729 AC: 30212 AN: 41464

American (AMR) AF: 0.797 AC: 12180 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2422 AN: 3466

East Asian (EAS) AF: 0.598 AC: 3078 AN: 5148

South Asian (SAS) AF: 0.628 AC: 3017 AN: 4802

European-Finnish (FIN) AF: 0.675 AC: 7127 AN: 10554

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48349 AN: 67912

Other (OTH) AF: 0.731 AC: 1546 AN: 2114

Alfa AF: 0.708 Hom.: 9638

Bravo AF: 0.725

Asia WGS AF: 0.633 AC: 2197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1335485; hg19: chr13-89015933;