chr17-14506849-C-T

Variant names:

• chr17-14506849-C-T
• rs2323284
• ENST00000700765.2:n.439-19336C>T

Variant summary

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

The ENST00000700765.2(ENSG00000230647):​n.439-19336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,828 control chromosomes in the GnomAD database, including 5,332 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 0.26 (5332 hom., cov: 32)
• Consequence: ENSG00000230647 ENST00000700765.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 4 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

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 (AFR) allele frequency at 95% confidence interval = 0.333 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
ENSG00000230647	ENST00000700765.2	n.439-19336C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39542 AN: 151710 Hom.: 5331 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.261 AC: 39566 AN: 151828 Hom.: 5332 Cov.: 32 AF XY: 0.262 AC XY: 19463 AN XY: 74196

African (AFR) AF: 0.337 AC: 13966 AN: 41388

American (AMR) AF: 0.212 AC: 3234 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5152

South Asian (SAS) AF: 0.218 AC: 1044 AN: 4794

European-Finnish (FIN) AF: 0.289 AC: 3034 AN: 10498

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15791 AN: 67934

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.236 Hom.: 2263

Bravo AF: 0.254

Asia WGS AF: 0.220 AC: 764 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	0.72
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2323284; hg19: chr17-14410166;