chr15-59750523-T-C

Variant names:

• chr15-59750523-T-C
• rs17269775

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 0.0417 in 152,204 control chromosomes in the GnomAD database, including 223 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 0.042 (223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0578 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: 0.0417 AC: 6343 AN: 152086 Hom.: 223 Cov.: 32

Gnomad AFR AF: 0.00961

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00831

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0417 AC: 6342 AN: 152204 Hom.: 223 Cov.: 32 AF XY: 0.0409 AC XY: 3044 AN XY: 74430

African (AFR) AF: 0.00960 AC: 399 AN: 41542

American (AMR) AF: 0.0498 AC: 761 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00831 AC: 40 AN: 4812

European-Finnish (FIN) AF: 0.0380 AC: 403 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4034 AN: 67996

Other (OTH) AF: 0.0583 AC: 123 AN: 2108

Alfa AF: 0.0484 Hom.: 234

Bravo AF: 0.0435

Asia WGS AF: 0.00664 AC: 24 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	1.3
DANN	Benign	0.53
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs17269775; hg19: chr15-60042722;