14-52259642-C-T

Variant names:

• chr14-52259642-C-T
• rs809722
• ENST00000835190.1:n.243-191G>A

Variant summary

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

The ENST00000835190.1(ENSG00000308586):​n.243-191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,170 control chromosomes in the GnomAD database, including 2,055 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 0.15 (2055 hom., cov: 32)
• Consequence: ENSG00000308586 ENST00000835190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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.243-191G>A		intron_variant	Intron 2 of 3
ENSG00000308586	ENST00000835191.1	n.258-191G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23430 AN: 152052 Hom.: 2057 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0849

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.154 AC: 23433 AN: 152170 Hom.: 2055 Cov.: 32 AF XY: 0.150 AC XY: 11197 AN XY: 74402

African (AFR) AF: 0.0896 AC: 3722 AN: 41520

American (AMR) AF: 0.138 AC: 2103 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5182

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4826

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10586

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14196 AN: 67994

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.184 Hom.: 8725

Bravo AF: 0.149

Asia WGS AF: 0.0580 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs809722; hg19: chr14-52726360;