14-96620760-G-A

Variant names:

• chr14-96620760-G-A
• rs234592
• ENST00000846020.1:n.51+27945G>A

Variant summary

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

The ENST00000846020.1(ENSG00000258702):​n.51+27945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,084 control chromosomes in the GnomAD database, including 26,117 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 0.58 (26117 hom., cov: 33)
• Consequence: ENSG00000258702 ENST00000846020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 5 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 = 0.687 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258702	ENST00000846020.1		n.51+27945G>A		intron	N/A
	ENSG00000258702	ENST00000846021.1		n.50+27945G>A		intron	N/A
	ENSG00000258702	ENST00000846022.1		n.54+27945G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87944 AN: 151966 Hom.: 26082 Cov.: 33

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.579 AC: 88034 AN: 152084 Hom.: 26117 Cov.: 33 AF XY: 0.579 AC XY: 43015 AN XY: 74330

African (AFR) AF: 0.694 AC: 28770 AN: 41472

American (AMR) AF: 0.449 AC: 6865 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2749 AN: 5162

South Asian (SAS) AF: 0.568 AC: 2739 AN: 4822

European-Finnish (FIN) AF: 0.640 AC: 6772 AN: 10588

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36916 AN: 67976

Other (OTH) AF: 0.522 AC: 1104 AN: 2114

Alfa AF: 0.546 Hom.: 45271

Bravo AF: 0.567

Asia WGS AF: 0.579 AC: 2011 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	0.023
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs234592; hg19: chr14-97087097;