15-95210724-C-T

Position:

• chr15-95210724-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.483 in 151,878 control chromosomes in the GnomAD database, including 20,502 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 0.48 (20502 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95210724C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LETR1	ENST00000556899.2	n.1165-83G>A		intron_variant		4
LETR1	ENST00000614853.2	n.620-83G>A		intron_variant		3
LETR1	ENST00000658041.1	n.506-83G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73263 AN: 151758 Hom.: 20463 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.445

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.483 AC: 73354 AN: 151876 Hom.: 20502 Cov.: 31 AF XY: 0.477 AC XY: 35396 AN XY: 74196

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.442

Alfa AF: 0.408 Hom.: 1915

Bravo AF: 0.494

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs290369; hg19: chr15-95753953;