5-36848456-C-T

Variant names:

• chr5-36848456-C-T
• rs158409

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 0.366 in 151,438 control chromosomes in the GnomAD database, including 10,518 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 0.37 (10518 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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: 0.365 AC: 55300 AN: 151320 Hom.: 10495 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.366 AC: 55365 AN: 151438 Hom.: 10518 Cov.: 31 AF XY: 0.370 AC XY: 27377 AN XY: 73980

African (AFR) AF: 0.469 AC: 19378 AN: 41278

American (AMR) AF: 0.364 AC: 5530 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1474 AN: 3464

East Asian (EAS) AF: 0.437 AC: 2245 AN: 5136

South Asian (SAS) AF: 0.405 AC: 1938 AN: 4790

European-Finnish (FIN) AF: 0.327 AC: 3421 AN: 10454

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20244 AN: 67834

Other (OTH) AF: 0.394 AC: 829 AN: 2106

Alfa AF: 0.326 Hom.: 1414

Bravo AF: 0.371

Asia WGS AF: 0.444 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.52
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs158409; hg19: chr5-36848558;