chr15-89937354-G-A

Position:

• chr15-89937354-G-A

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 0.738 in 151,974 control chromosomes in the GnomAD database, including 45,824 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 0.74 (45824 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.739 AC: 112222 AN: 151854 Hom.: 45839 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.738 AC: 112201 AN: 151974 Hom.: 45824 Cov.: 31 AF XY: 0.736 AC XY: 54672 AN XY: 74274

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.794

Alfa AF: 0.901 Hom.: 108057

Bravo AF: 0.705

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1702161; hg19: chr15-90480586;