ENST00000746096.1:n.190-5240T>C

Variant names:

• chr17-50632580-A-G
• rs8073706
• ENST00000746096.1:n.190-5240T>C

Variant summary

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

The ENST00000746096.1(ENSG00000251239):​n.190-5240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,996 control chromosomes in the GnomAD database, including 18,025 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 0.46 (18025 hom., cov: 32)
• Consequence: ENSG00000251239 ENST00000746096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 5 publications found

Genes affected

ENSG00000251239 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746096.1. 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
	ENSG00000251239	ENST00000746096.1		n.190-5240T>C		intron	N/A
	ENSG00000297214	ENST00000746227.1		n.363+434A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70554 AN: 151878 Hom.: 18008 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.465 AC: 70624 AN: 151996 Hom.: 18025 Cov.: 32 AF XY: 0.472 AC XY: 35086 AN XY: 74314

African (AFR) AF: 0.585 AC: 24222 AN: 41436

American (AMR) AF: 0.567 AC: 8661 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4720 AN: 5168

South Asian (SAS) AF: 0.610 AC: 2941 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3640 AN: 10586

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23546 AN: 67926

Other (OTH) AF: 0.455 AC: 957 AN: 2104

Alfa AF: 0.457 Hom.: 5428

Bravo AF: 0.486

Asia WGS AF: 0.782 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.62
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs8073706; hg19: chr17-48709941;