15-46478763-G-T

Position:

• chr15-46478763-G-T

Variant summary

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

The ENST00000686120.1(ENSG00000287704):​n.56+68410G>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 0.434 in 151,236 control chromosomes in the GnomAD database, including 16,187 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 0.43 (16187 hom., cov: 30)
• Consequence: ENST00000686120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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
	ENST00000686120.1	n.56+68410G>T		intron_variant, non_coding_transcript_variant
	ENST00000661853.1	n.45+68410G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65599 AN: 151120 Hom.: 16196 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.434 AC: 65588 AN: 151236 Hom.: 16187 Cov.: 30 AF XY: 0.435 AC XY: 32108 AN XY: 73882

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.468

Alfa AF: 0.494 Hom.: 2498

Bravo AF: 0.419

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1120650; hg19: chr15-46770961;