rs28373064

chr1-206117775-T-C

Variant summary

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

The XR_007066828.1(LOC124904492):n.99T>C 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 0.186 in 152,110 control chromosomes in the GnomAD database, including 2,882 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 0.19 (2881 hom., cov: 31)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: LOC124904492 XR_007066828.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

LOC124904492 (HGNC:):

AVPR1B-DT (HGNC:55832): (AVPR1B divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904492	XR_007066828.1	n.99T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1B-DT	ENST00000425896.1			upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28285 AN: 151924 Hom.: 2877 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.121 AC: 8 AN: 66 Hom.: 1 Cov.: 0 AF XY: 0.104 AC XY: 5 AN XY: 48

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.133

GnomAD4 genome AF: 0.186 AC: 28316 AN: 152044 Hom.: 2881 Cov.: 31 AF XY: 0.187 AC XY: 13866 AN XY: 74310

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.188

Alfa AF: 0.161 Hom.: 1884

Bravo AF: 0.187

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28373064; hg19: chr1-206223556;