chr15-91852033-A-T

Position:

• chr15-91852033-A-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 0.352 in 152,060 control chromosomes in the GnomAD database, including 13,067 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 0.35 (13067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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: 0.351 AC: 53384 AN: 151942 Hom.: 13019 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.352 AC: 53490 AN: 152060 Hom.: 13067 Cov.: 32 AF XY: 0.342 AC XY: 25468 AN XY: 74362

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0919

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.326

Alfa AF: 0.276 Hom.: 1022

Bravo AF: 0.375

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11858120; hg19: chr15-92395263;