rs9595049

chr13-44019775-G-T

Variant summary

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

The ENST00000439707.6(NRAD1):n.100-2700G>T 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 0.291 in 152,092 control chromosomes in the GnomAD database, including 8,057 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 0.29 (8057 hom., cov: 32)
• Consequence: NRAD1 ENST00000439707.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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.100-2700G>T		intron_variant, non_coding_transcript_variant		5
NRAD1	ENST00000585327.5	n.255-2700G>T		intron_variant, non_coding_transcript_variant		5
NRAD1	ENST00000620454.4	n.349-2700G>T		intron_variant, non_coding_transcript_variant		4
NRAD1	ENST00000629019.2	n.109-2700G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44261 AN: 151974 Hom.: 8060 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.291 AC: 44246 AN: 152092 Hom.: 8057 Cov.: 32 AF XY: 0.287 AC XY: 21323 AN XY: 74330

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.293

Alfa AF: 0.383 Hom.: 12533

Bravo AF: 0.270

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.64

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: rs9595049; hg19: chr13-44593911;