ENST00000624514.1:n.2028A>G

Variant names:

• chr17-18108436-T-C
• rs854764
• ENST00000624514.1:n.2028A>G

Variant summary

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

The ENST00000624514.1(ENSG00000279428):​n.2028A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,294 control chromosomes in the GnomAD database, including 15,523 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 0.40 (15456 hom., cov: 31)
  • Exomes 𝑓: 0.59 (67 hom.)
• Consequence: ENSG00000279428 ENST00000624514.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

Genes affected

ENSG00000279428 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371566	NR_164159.1	n.647A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279428	ENST00000624514.1	n.2028A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60539 AN: 151804 Hom.: 15454 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.589 AC: 219 AN: 372 Hom.: 67 Cov.: 0 AF XY: 0.570 AC XY: 171 AN XY: 300

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.605

Gnomad4 OTH exome AF: 0.643

GnomAD4 genome AF: 0.398 AC: 60534 AN: 151922 Hom.: 15456 Cov.: 31 AF XY: 0.388 AC XY: 28817 AN XY: 74254

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.0658

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.432

Alfa AF: 0.507 Hom.: 7188

Bravo AF: 0.383

Asia WGS AF: 0.187 AC: 654 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	0.64
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854764; hg19: chr17-18011750;