ENST00000661853.1:n.45+68410G>T

Variant names:

• chr15-46478763-G-T
• rs1120650
• ENST00000661853.1:n.45+68410G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661853.1(ENSG00000287704):​n.45+68410G>T variant causes a intron 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: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 1 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661853.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287704	ENST00000661853.1		n.45+68410G>T		intron	N/A
	ENSG00000287704	ENST00000686120.1		n.56+68410G>T		intron	N/A
	ENSG00000287704	ENST00000736459.1		n.46+68410G>T		intron	N/A

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

African (AFR) AF: 0.182 AC: 7531 AN: 41326

American (AMR) AF: 0.458 AC: 6921 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2068 AN: 3460

East Asian (EAS) AF: 0.563 AC: 2872 AN: 5100

South Asian (SAS) AF: 0.463 AC: 2221 AN: 4802

European-Finnish (FIN) AF: 0.514 AC: 5422 AN: 10542

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 36916 AN: 67606

Other (OTH) AF: 0.468 AC: 979 AN: 2090

Alfa AF: 0.482 Hom.: 2515

Bravo AF: 0.419

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.18
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1120650; hg19: chr15-46770961;