15-93465926-C-T

Position:

• chr15-93465926-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667030.1(ENSG00000257060):​n.237-30308C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0412 in 152,126 control chromosomes in the GnomAD database, including 352 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 0.041 (352 hom., cov: 32)
• Consequence: ENST00000667030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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
	ENST00000667030.1	n.237-30308C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 6242 AN: 152008 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0412 AC: 6262 AN: 152126 Hom.: 352 Cov.: 32 AF XY: 0.0437 AC XY: 3253 AN XY: 74364

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0338 Hom.: 155

Bravo AF: 0.0461

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17651761; hg19: chr15-94009155;