rs483082

Variant names:

• chr19-44912921-G-T
• rs483082
• ENST00000623895.1:n.3547G>T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3547G>T 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 0.273 in 152,284 control chromosomes in the GnomAD database, including 6,692 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 0.27 (6691 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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
ENSG00000280087	ENST00000623895.1	n.3547G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41476 AN: 151906 Hom.: 6672 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.119 AC: 31 AN: 260 Hom.: 1 Cov.: 0 AF XY: 0.120 AC XY: 24 AN XY: 200

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.0833

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.273 AC: 41547 AN: 152024 Hom.: 6691 Cov.: 32 AF XY: 0.270 AC XY: 20079 AN XY: 74300

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.230

Alfa AF: 0.282 Hom.: 994

Bravo AF: 0.276

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs483082; hg19: chr19-45416178;