13-43933553-T-C

Variant names:

• chr13-43933553-T-C
• rs687582
• ENST00000627615.1:n.*500-8039T>C

Variant summary

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

The ENST00000627615.1(ENSG00000281883):​n.*500-8039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,030 control chromosomes in the GnomAD database, including 7,254 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 0.30 (7254 hom., cov: 32)
• Consequence: ENSG00000281883 ENST00000627615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

Genes affected

ENSG00000281883 (HGNC:):

NRAD1 (HGNC:26981): (non-coding RNA in the aldehyde dehydrogenase 1A pathway)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 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
ENSG00000281883	ENST00000627615.1	n.*500-8039T>C		intron_variant	Intron 7 of 12	5		ENSP00000486083.1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44951 AN: 151912 Hom.: 7224 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.296 AC: 45028 AN: 152030 Hom.: 7254 Cov.: 32 AF XY: 0.301 AC XY: 22394 AN XY: 74322

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.321

Alfa AF: 0.241 Hom.: 9541

Bravo AF: 0.307

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs687582; hg19: chr13-44507689;