14-52301407-A-G

Variant names:

• chr14-52301407-A-G
• rs8006060
• ENST00000726797.1:n.299+11429T>C

Variant summary

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

The ENST00000726797.1(ENSG00000289424):​n.299+11429T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,948 control chromosomes in the GnomAD database, including 9,046 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 0.30 (9046 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000726797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 2 publications found

Genes affected

ENSG00000289424 (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 = 0.559 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
ENSG00000289424	ENST00000726797.1	n.299+11429T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45379 AN: 151830 Hom.: 9011 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.299 AC: 45475 AN: 151948 Hom.: 9046 Cov.: 32 AF XY: 0.307 AC XY: 22801 AN XY: 74270

African (AFR) AF: 0.505 AC: 20889 AN: 41384

American (AMR) AF: 0.390 AC: 5958 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2975 AN: 5158

South Asian (SAS) AF: 0.450 AC: 2166 AN: 4814

European-Finnish (FIN) AF: 0.176 AC: 1855 AN: 10566

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10011 AN: 67958

Other (OTH) AF: 0.282 AC: 595 AN: 2108

Alfa AF: 0.190 Hom.: 3817

Bravo AF: 0.324

Asia WGS AF: 0.479 AC: 1667 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	0.84
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8006060; hg19: chr14-52768125;