15-84812263-C-T

Variant names:

• chr15-84812263-C-T
• rs8037423

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.549 in 151,842 control chromosomes in the GnomAD database, including 23,877 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 0.55 (23877 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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: 0.548 AC: 83219 AN: 151726 Hom.: 23836 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.549 AC: 83317 AN: 151842 Hom.: 23877 Cov.: 31 AF XY: 0.550 AC XY: 40828 AN XY: 74180

African (AFR) AF: 0.708 AC: 29320 AN: 41420

American (AMR) AF: 0.533 AC: 8135 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1555 AN: 3466

East Asian (EAS) AF: 0.790 AC: 4064 AN: 5146

South Asian (SAS) AF: 0.538 AC: 2584 AN: 4804

European-Finnish (FIN) AF: 0.458 AC: 4823 AN: 10532

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31362 AN: 67912

Other (OTH) AF: 0.507 AC: 1066 AN: 2104

Alfa AF: 0.459 Hom.: 7771

Bravo AF: 0.559

Asia WGS AF: 0.667 AC: 2318 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	0.81
DANN	Benign	0.41
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs8037423; hg19: chr15-85355494;