15-75155432-C-T

Variant names:

• chr15-75155432-C-T
• rs8027604

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 0.696 in 152,084 control chromosomes in the GnomAD database, including 37,103 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 0.70 (37103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.695 AC: 105688 AN: 151966 Hom.: 37050 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.696 AC: 105800 AN: 152084 Hom.: 37103 Cov.: 32 AF XY: 0.692 AC XY: 51407 AN XY: 74338

African (AFR) AF: 0.766 AC: 31800 AN: 41502

American (AMR) AF: 0.717 AC: 10949 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4005 AN: 5162

South Asian (SAS) AF: 0.694 AC: 3346 AN: 4822

European-Finnish (FIN) AF: 0.547 AC: 5783 AN: 10566

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45030 AN: 67962

Other (OTH) AF: 0.732 AC: 1549 AN: 2116

Alfa AF: 0.667 Hom.: 21348

Bravo AF: 0.712

Asia WGS AF: 0.784 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs8027604; hg19: chr15-75447773;