rs13329271

chr15-78621888-A-Cchr15-78621888-A-Gchr15-78621888-A-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 0.272 in 152,006 control chromosomes in the GnomAD database, including 6,290 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 0.27 (6290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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: 0.272 AC: 41287 AN: 151886 Hom.: 6269 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.272 AC: 41340 AN: 152006 Hom.: 6290 Cov.: 32 AF XY: 0.279 AC XY: 20715 AN XY: 74310

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.283

Alfa AF: 0.248 Hom.: 623

Bravo AF: 0.286

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13329271; hg19: chr15-78914230;