3-180201290-T-C

Variant names:

• chr3-180201290-T-C
• rs4854964
• ENST00000633048.1:n.*78T>C

Variant summary

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

The ENST00000633048.1(ENSG00000282327):​n.*78T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,984 control chromosomes in the GnomAD database, including 10,359 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 0.35 (10359 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000282327 ENST00000633048.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

ENSG00000282327 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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
ENSG00000282327	ENST00000633048.1	n.*78T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52522 AN: 151866 Hom.: 10331 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.346 AC: 52602 AN: 151984 Hom.: 10359 Cov.: 32 AF XY: 0.351 AC XY: 26093 AN XY: 74328

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.331

Alfa AF: 0.253 Hom.: 10412

Bravo AF: 0.359

Asia WGS AF: 0.457 AC: 1588 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4854964; hg19: chr3-179919078;