14-76147335-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

Genes affected

ENSG00000283629 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.657 AC: 27243 AN: 41468

American (AMR) AF: 0.842 AC: 12877 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4193 AN: 5178

South Asian (SAS) AF: 0.879 AC: 4241 AN: 4826

European-Finnish (FIN) AF: 0.856 AC: 9065 AN: 10588

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57076 AN: 68002

Other (OTH) AF: 0.761 AC: 1607 AN: 2112

Alfa AF: 0.820 Hom.: 242238

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs935334; hg19: chr14-76613678;