14-52267266-T-C

Variant names:

• chr14-52267266-T-C
• rs8004654
• ENST00000835190.1:n.143+170A>G

Variant summary

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

The ENST00000835190.1(ENSG00000308586):​n.143+170A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,010 control chromosomes in the GnomAD database, including 20,394 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 0.51 (20394 hom., cov: 31)
• Consequence: ENSG00000308586 ENST00000835190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 21 publications found

Genes affected

ENSG00000308586 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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
ENSG00000308586	ENST00000835190.1	n.143+170A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77723 AN: 151892 Hom.: 20362 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.512 AC: 77801 AN: 152010 Hom.: 20394 Cov.: 31 AF XY: 0.508 AC XY: 37748 AN XY: 74304

African (AFR) AF: 0.555 AC: 23004 AN: 41424

American (AMR) AF: 0.402 AC: 6146 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2035 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1452 AN: 5156

South Asian (SAS) AF: 0.574 AC: 2764 AN: 4818

European-Finnish (FIN) AF: 0.487 AC: 5148 AN: 10570

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35246 AN: 67966

Other (OTH) AF: 0.528 AC: 1114 AN: 2108

Alfa AF: 0.518 Hom.: 35397

Bravo AF: 0.501

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.30
PhyloP100		-0.33
PromoterAI		0.0025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8004654; hg19: chr14-52733984;