15-23805058-T-C

Position:

• chr15-23805058-T-C

Variant summary

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

The ENST00000658937.1(ENSG00000286973):​n.460-19666T>C 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 0.163 in 151,048 control chromosomes in the GnomAD database, including 2,357 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 0.16 (2357 hom., cov: 32)
• Consequence: ENST00000658937.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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
	ENST00000658937.1	n.460-19666T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24656 AN: 150930 Hom.: 2346 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.163 AC: 24686 AN: 151048 Hom.: 2357 Cov.: 32 AF XY: 0.158 AC XY: 11669 AN XY: 73876

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0306

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.171

Alfa AF: 0.0525 Hom.: 52

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519449; hg19: chr15-24050205;