14-76147335-T-C

Variant names:

• chr14-76147335-T-C
• rs935334
• ENST00000636059.1:n.106+5187A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636059.1(ENSG00000283629):​n.106+5187A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,140 control chromosomes in the GnomAD database, including 47,687 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 0.79 (47687 hom., cov: 32)
• Consequence: ENSG00000283629 ENST00000636059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

Genes affected

ENSG00000283629 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.857 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
ENSG00000283629	ENST00000636059.1	n.106+5187A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119561 AN: 152022 Hom.: 47650 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.786 AC: 119654 AN: 152140 Hom.: 47687 Cov.: 32 AF XY: 0.789 AC XY: 58707 AN XY: 74378

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.761

Alfa AF: 0.823 Hom.: 121385

Bravo AF: 0.779

Asia WGS AF: 0.840 AC: 2921 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	4.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs935334; hg19: chr14-76613678;