15-90868426-C-T

Position:

• chr15-90868426-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 0.314 in 152,006 control chromosomes in the GnomAD database, including 7,712 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 0.31 (7712 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90868426C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47642 AN: 151888 Hom.: 7706 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.314 AC: 47658 AN: 152006 Hom.: 7712 Cov.: 32 AF XY: 0.308 AC XY: 22922 AN XY: 74310

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.314

Alfa AF: 0.352 Hom.: 13378

Bravo AF: 0.309

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4932178; hg19: chr15-91411656;