chr13-36843290-A-C

Variant names:

• chr13-36843290-A-C
• rs609418

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 0.363 in 151,488 control chromosomes in the GnomAD database, including 11,764 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 0.36 (11764 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.363 AC: 54946 AN: 151376 Hom.: 11726 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.363 AC: 55046 AN: 151488 Hom.: 11764 Cov.: 31 AF XY: 0.365 AC XY: 26992 AN XY: 74012

African (AFR) AF: 0.594 AC: 24469 AN: 41178

American (AMR) AF: 0.269 AC: 4094 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3464

East Asian (EAS) AF: 0.428 AC: 2194 AN: 5132

South Asian (SAS) AF: 0.413 AC: 1979 AN: 4796

European-Finnish (FIN) AF: 0.269 AC: 2810 AN: 10456

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17139 AN: 67934

Other (OTH) AF: 0.360 AC: 756 AN: 2100

Alfa AF: 0.292 Hom.: 21905

Bravo AF: 0.371

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs609418; hg19: chr13-37417427;