chr14-20879073-C-T

Variant names:

• chr14-20879073-C-T
• rs11156734
• ENST00000717679.1:n.259-3330G>A

Variant summary

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

The ENST00000717679.1(ENSG00000259130):​n.259-3330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,114 control chromosomes in the GnomAD database, including 32,520 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 0.62 (32520 hom., cov: 32)
• Consequence: ENSG00000259130 ENST00000717679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 4 publications found

Genes affected

ENSG00000259130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717679.1. 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
	ENSG00000259130	ENST00000717679.1		n.259-3330G>A		intron	N/A
	ENSG00000259130	ENST00000717680.1		n.347-3330G>A		intron	N/A
	ENSG00000259130	ENST00000717681.1		n.285-3330G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94552 AN: 151996 Hom.: 32505 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.622 AC: 94605 AN: 152114 Hom.: 32520 Cov.: 32 AF XY: 0.628 AC XY: 46675 AN XY: 74352

African (AFR) AF: 0.302 AC: 12518 AN: 41492

American (AMR) AF: 0.784 AC: 11983 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3142 AN: 5150

South Asian (SAS) AF: 0.757 AC: 3648 AN: 4816

European-Finnish (FIN) AF: 0.746 AC: 7889 AN: 10576

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50662 AN: 68000

Other (OTH) AF: 0.652 AC: 1378 AN: 2114

Alfa AF: 0.684 Hom.: 4709

Bravo AF: 0.608

Asia WGS AF: 0.677 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.41
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs11156734; hg19: chr14-21347232;