13-59609913-C-T

Variant names:

• chr13-59609913-C-T
• rs505299

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 0.877 in 152,178 control chromosomes in the GnomAD database, including 59,949 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 0.88 (59949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.962 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: 0.878 AC: 133447 AN: 152060 Hom.: 59928 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.877 AC: 133519 AN: 152178 Hom.: 59949 Cov.: 32 AF XY: 0.881 AC XY: 65529 AN XY: 74410

African (AFR) AF: 0.662 AC: 27451 AN: 41480

American (AMR) AF: 0.936 AC: 14320 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3292 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4583 AN: 5166

South Asian (SAS) AF: 0.941 AC: 4530 AN: 4816

European-Finnish (FIN) AF: 0.981 AC: 10405 AN: 10610

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65882 AN: 68026

Other (OTH) AF: 0.891 AC: 1881 AN: 2112

Alfa AF: 0.943 Hom.: 92637

Bravo AF: 0.864

Asia WGS AF: 0.900 AC: 3129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.36
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs505299; hg19: chr13-60184047;