chr13-43941285-T-A

Variant names:

• chr13-43941285-T-A
• rs895265
• ENST00000627615.1:n.*500-307T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000627615.1(ENSG00000281883):​n.*500-307T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,064 control chromosomes in the GnomAD database, including 6,377 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 0.28 (6377 hom., cov: 32)
• Consequence: ENSG00000281883 ENST00000627615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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.*500-307T>A		intron	N/A	ENSP00000486083.1
	NRAD1	ENST00000439707.6	TSL:5	n.99+21852T>A		intron	N/A
	NRAD1	ENST00000585327.5	TSL:5	n.64-1138T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42399 AN: 151946 Hom.: 6350 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.279 AC: 42472 AN: 152064 Hom.: 6377 Cov.: 32 AF XY: 0.285 AC XY: 21196 AN XY: 74356

African (AFR) AF: 0.330 AC: 13691 AN: 41462

American (AMR) AF: 0.324 AC: 4957 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2660 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2461 AN: 10594

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

European-Non Finnish (NFE) AF: 0.223 AC: 15185 AN: 67962

Other (OTH) AF: 0.310 AC: 655 AN: 2112

Alfa AF: 0.246 Hom.: 596

Bravo AF: 0.288

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.82
DANN	Benign	0.88
PhyloP100		-2.2

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: rs895265; hg19: chr13-44515421;