15-74804102-T-C

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 0.64 in 152,082 control chromosomes in the GnomAD database, including 31,702 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 0.64 (31702 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.640 AC: 97286 AN: 151964 Hom.: 31699 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.640 AC: 97331 AN: 152082 Hom.: 31702 Cov.: 33 AF XY: 0.635 AC XY: 47209 AN XY: 74370

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.626

Alfa AF: 0.685 Hom.: 35181

Bravo AF: 0.627

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378938; hg19: chr15-75096443;