rs13329271

Variant names:

• chr15-78621888-A-C
• rs13329271

Your query was ambiguous. Multiple possible variants found:

• chr15-78621888-A-C
• chr15-78621888-A-G
• chr15-78621888-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;