15-74373173-C-T

Position:

• chr15-74373173-C-T

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 0.623 in 152,042 control chromosomes in the GnomAD database, including 30,015 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 0.62 (30015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94679 AN: 151924 Hom.: 30013 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.623 AC: 94715 AN: 152042 Hom.: 30015 Cov.: 33 AF XY: 0.619 AC XY: 45998 AN XY: 74300

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.606

Alfa AF: 0.662 Hom.: 4940

Bravo AF: 0.614

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077581; hg19: chr15-74665514;