15-74942269-T-C

Variant names:

• chr15-74942269-T-C
• rs11072518

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 0.574 in 151,688 control chromosomes in the GnomAD database, including 25,408 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 0.57 (25408 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 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: 0.574 AC: 86956 AN: 151570 Hom.: 25384 Cov.: 29

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.574 AC: 87023 AN: 151688 Hom.: 25408 Cov.: 29 AF XY: 0.562 AC XY: 41665 AN XY: 74096

African (AFR) AF: 0.537 AC: 22232 AN: 41370

American (AMR) AF: 0.548 AC: 8340 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2597 AN: 5122

South Asian (SAS) AF: 0.285 AC: 1364 AN: 4790

European-Finnish (FIN) AF: 0.527 AC: 5544 AN: 10520

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42917 AN: 67890

Other (OTH) AF: 0.578 AC: 1211 AN: 2096

Alfa AF: 0.606 Hom.: 76232

Bravo AF: 0.582

Asia WGS AF: 0.420 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11072518; hg19: chr15-75234610;