rs895265

chr13-43941285-T-A

Variant summary

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

The ENST00000439707.6(NRAD1):n.99+21852T>A variant causes a intron, non coding transcript 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: NRAD1 ENST00000439707.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRAD1	ENST00000439707.6	n.99+21852T>A		intron_variant, non_coding_transcript_variant		5
NRAD1	ENST00000585327.5	n.64-1138T>A		intron_variant, non_coding_transcript_variant		5
NRAD1	ENST00000620454.4	n.158-1138T>A		intron_variant, non_coding_transcript_variant		4
NRAD1	ENST00000629019.2	n.108+19606T>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.310

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.82
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: rs895265; hg19: chr13-44515421;