15-89037068-C-G

Position:

• chr15-89037068-C-G

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 0.298 in 151,808 control chromosomes in the GnomAD database, including 11,755 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 0.30 (11755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.298 AC: 45182 AN: 151690 Hom.: 11699 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.298 AC: 45305 AN: 151808 Hom.: 11755 Cov.: 32 AF XY: 0.301 AC XY: 22364 AN XY: 74178

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.263

Alfa AF: 0.190 Hom.: 739

Bravo AF: 0.334

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
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: rs2351254; hg19: chr15-89580299;