13-43933553-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000281883 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000627615.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281883	ENST00000627615.1	TSL:5	n.*500-8039T>C		intron	N/A	ENSP00000486083.1
	NRAD1	ENST00000439707.6	TSL:5	n.99+14120T>C		intron	N/A
	NRAD1	ENST00000585327.5	TSL:5	n.64-8870T>C		intron	N/A

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

African (AFR) AF: 0.391 AC: 16221 AN: 41476

American (AMR) AF: 0.330 AC: 5039 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3460

East Asian (EAS) AF: 0.516 AC: 2662 AN: 5158

South Asian (SAS) AF: 0.321 AC: 1543 AN: 4802

European-Finnish (FIN) AF: 0.232 AC: 2457 AN: 10598

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15115 AN: 67954

Other (OTH) AF: 0.321 AC: 675 AN: 2106

Alfa AF: 0.251 Hom.: 15651

Bravo AF: 0.307

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		-0.98

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

Other links and lift over

dbSNP: rs687582; hg19: chr13-44507689;