13-44040903-G-A

Variant names:

• chr13-44040903-G-A
• rs7323018
• ENST00000772210.1:n.762+630G>A

Variant summary

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

The ENST00000772210.1(NRAD1):​n.762+630G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,068 control chromosomes in the GnomAD database, including 29,036 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 0.59 (29036 hom., cov: 33)
• Consequence: NRAD1 ENST00000772210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 7 publications found

Genes affected

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772210.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRAD1	ENST00000772210.1		n.762+630G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89088 AN: 151950 Hom.: 29034 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.586 AC: 89110 AN: 152068 Hom.: 29036 Cov.: 33 AF XY: 0.585 AC XY: 43512 AN XY: 74332

African (AFR) AF: 0.279 AC: 11563 AN: 41484

American (AMR) AF: 0.693 AC: 10581 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3466

East Asian (EAS) AF: 0.682 AC: 3525 AN: 5172

South Asian (SAS) AF: 0.517 AC: 2492 AN: 4822

European-Finnish (FIN) AF: 0.743 AC: 7868 AN: 10590

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.723 AC: 49144 AN: 67950

Other (OTH) AF: 0.616 AC: 1302 AN: 2114

Alfa AF: 0.679 Hom.: 154395

Bravo AF: 0.575

Asia WGS AF: 0.593 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7323018; hg19: chr13-44615039;