15-89037068-C-G

Variant names:

• chr15-89037068-C-G
• rs2351254

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;