15-99817230-T-C

Position:

• chr15-99817230-T-C

Variant summary

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

The ENST00000665821.1(ENSG00000259363):​n.863T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,112 control chromosomes in the GnomAD database, including 13,885 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 0.42 (13885 hom., cov: 32)
• Consequence: ENSG00000259363 ENST00000665821.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

ENSG00000259363 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC400464	NR_135737.1	n.346+4144T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259363	ENST00000665821.1	n.863T>C		non_coding_transcript_exon_variant	3/3
ENSG00000259363	ENST00000558188.2	n.589+4144T>C		intron_variant		3
ENSG00000259363	ENST00000559714.6	n.319+4144T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64273 AN: 151994 Hom.: 13870 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.423 AC: 64319 AN: 152112 Hom.: 13885 Cov.: 32 AF XY: 0.419 AC XY: 31136 AN XY: 74360

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.396

Alfa AF: 0.409 Hom.: 24816

Bravo AF: 0.422

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823874; hg19: chr15-100357435;