5-13242862-C-T

Variant names:

• chr5-13242862-C-T
• rs10066447

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 0.251 in 151,954 control chromosomes in the GnomAD database, including 4,895 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 0.25 (4895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 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: 0.250 AC: 38024 AN: 151838 Hom.: 4883 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.251 AC: 38078 AN: 151954 Hom.: 4895 Cov.: 32 AF XY: 0.249 AC XY: 18479 AN XY: 74266

African (AFR) AF: 0.268 AC: 11093 AN: 41436

American (AMR) AF: 0.178 AC: 2717 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1712 AN: 5168

South Asian (SAS) AF: 0.113 AC: 545 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3075 AN: 10540

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17272 AN: 67936

Other (OTH) AF: 0.249 AC: 524 AN: 2104

Alfa AF: 0.246 Hom.: 11440

Bravo AF: 0.244

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.18
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10066447; hg19: chr5-13242974;