rs483082

Positions:

• chr19-44912921-G-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/exons	MANE	Protein	UniProt
		n.44912921G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.3547G>T		non_coding_transcript_exon_variant	1/1	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;