rs8023715

chr15-97064451-C-Achr15-97064451-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 0.0833 in 152,106 control chromosomes in the GnomAD database, including 569 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 0.083 (569 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0987 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: 0.0833 AC: 12667 AN: 151988 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0833 AC: 12676 AN: 152106 Hom.: 569 Cov.: 33 AF XY: 0.0823 AC XY: 6118 AN XY: 74372

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0717

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0760 Hom.: 649

Bravo AF: 0.0840

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.69
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8023715; hg19: chr15-97607681;