rs10066447

chr5-13242862-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.249

Alfa AF: 0.247 Hom.: 6966

Bravo AF: 0.244

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.5
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10066447; hg19: chr5-13242974;