14-39007303-C-T

Variant names:

• chr14-39007303-C-T
• rs8014021
• ENST00000828713.1:n.126-3007G>A

Variant summary

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

The ENST00000828713.1(ENSG00000307769):​n.126-3007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,156 control chromosomes in the GnomAD database, including 58,300 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 0.87 (58300 hom., cov: 31)
• Consequence: ENSG00000307769 ENST00000828713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699
• Publications: 3 publications found

Genes affected

ENSG00000307769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307769	ENST00000828713.1	n.126-3007G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132858 AN: 152038 Hom.: 58262 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.874 AC: 132948 AN: 152156 Hom.: 58300 Cov.: 31 AF XY: 0.869 AC XY: 64654 AN XY: 74358

African (AFR) AF: 0.901 AC: 37393 AN: 41518

American (AMR) AF: 0.834 AC: 12749 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2935 AN: 3472

East Asian (EAS) AF: 0.972 AC: 5030 AN: 5176

South Asian (SAS) AF: 0.700 AC: 3366 AN: 4806

European-Finnish (FIN) AF: 0.892 AC: 9423 AN: 10566

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59226 AN: 68016

Other (OTH) AF: 0.846 AC: 1789 AN: 2114

Alfa AF: 0.860 Hom.: 35914

Bravo AF: 0.875

Asia WGS AF: 0.835 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.29
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs8014021; hg19: chr14-39476507;