ENST00000846020.1:n.52-43725G>A

Variant names:

• chr14-96637470-G-A
• rs17094273
• ENST00000846020.1:n.52-43725G>A

Variant summary

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

The ENST00000846020.1(ENSG00000258702):​n.52-43725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,150 control chromosomes in the GnomAD database, including 2,068 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 0.15 (2068 hom., cov: 34)
• Consequence: ENSG00000258702 ENST00000846020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 17 publications found

Genes affected

ENSG00000258702 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846020.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258702	ENST00000846020.1		n.52-43725G>A		intron	N/A
	ENSG00000258702	ENST00000846021.1		n.51-29925G>A		intron	N/A
	ENSG00000258702	ENST00000846022.1		n.55-29925G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22584 AN: 152030 Hom.: 2063 Cov.: 34

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.149 AC: 22630 AN: 152150 Hom.: 2068 Cov.: 34 AF XY: 0.148 AC XY: 10972 AN XY: 74376

African (AFR) AF: 0.252 AC: 10475 AN: 41492

American (AMR) AF: 0.102 AC: 1554 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.154 AC: 795 AN: 5176

South Asian (SAS) AF: 0.202 AC: 974 AN: 4824

European-Finnish (FIN) AF: 0.0950 AC: 1005 AN: 10582

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7155 AN: 68004

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.113 Hom.: 2217

Bravo AF: 0.152

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.26
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17094273; hg19: chr14-97103807;