ENST00000768252.1:n.138-13949C>T

Variant names:

• chr14-68758968-G-A
• rs451066
• ENST00000768252.1:n.138-13949C>T

Variant summary

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

The ENST00000768252.1(ENSG00000289583):​n.138-13949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,016 control chromosomes in the GnomAD database, including 2,593 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 0.17 (2593 hom., cov: 32)
• Consequence: ENSG00000289583 ENST00000768252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 7 publications found

Genes affected

ENSG00000289583 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768252.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289583	ENST00000768252.1		n.138-13949C>T		intron	N/A
	ENSG00000289583	ENST00000768253.1		n.246+8778C>T		intron	N/A
	ENSG00000289583	ENST00000768254.1		n.233+8778C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25307 AN: 151898 Hom.: 2595 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.167 AC: 25316 AN: 152016 Hom.: 2593 Cov.: 32 AF XY: 0.164 AC XY: 12225 AN XY: 74324

African (AFR) AF: 0.0682 AC: 2828 AN: 41478

American (AMR) AF: 0.274 AC: 4179 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.150 AC: 773 AN: 5150

South Asian (SAS) AF: 0.170 AC: 818 AN: 4810

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14104 AN: 67944

Other (OTH) AF: 0.169 AC: 355 AN: 2106

Alfa AF: 0.183 Hom.: 831

Bravo AF: 0.180

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.36
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs451066; hg19: chr14-69225685;