13-59623595-T-C

Variant names:

• chr13-59623595-T-C
• rs343129

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.861 in 152,186 control chromosomes in the GnomAD database, including 58,229 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 0.86 (58229 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 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: 0.862 AC: 131052 AN: 152068 Hom.: 58213 Cov.: 33

Gnomad AFR AF: 0.617

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.861 AC: 131103 AN: 152186 Hom.: 58229 Cov.: 33 AF XY: 0.864 AC XY: 64335 AN XY: 74422

African (AFR) AF: 0.616 AC: 25555 AN: 41472

American (AMR) AF: 0.929 AC: 14217 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3189 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4595 AN: 5182

South Asian (SAS) AF: 0.918 AC: 4418 AN: 4812

European-Finnish (FIN) AF: 0.979 AC: 10393 AN: 10614

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65713 AN: 68026

Other (OTH) AF: 0.876 AC: 1847 AN: 2108

Alfa AF: 0.878 Hom.: 4399

Bravo AF: 0.847

Asia WGS AF: 0.881 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	15
DANN	Benign	0.71
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs343129; hg19: chr13-60197729;