5-111941787-G-T

Variant summary

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

The NR_046678.1(NREP-AS1):n.311+1653G>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 0.537 in 151,842 control chromosomes in the GnomAD database, including 22,977 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 0.54 (22977 hom., cov: 32)
• Consequence: NREP-AS1 NR_046678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

NREP-AS1 (HGNC:40780): (NREP antisense RNA 1)

NREP (HGNC:16834): (neuronal regeneration related protein) Predicted to be involved in axon regeneration; regulation of neuron differentiation; and regulation of transforming growth factor beta receptor signaling pathway. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NREP-AS1	NR_046678.1	n.311+1653G>T		intron_variant, non_coding_transcript_variant
NREP	NM_001142474.2	c.105+33517C>A		intron_variant
NREP	NM_001142475.2	c.135+33487C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NREP-AS1	ENST00000507222.5	n.311+1653G>T		intron_variant, non_coding_transcript_variant		3
NREP	ENST00000395634.7	c.135+33487C>A		intron_variant		2
NREP	ENST00000450761.6	c.-59+55537C>A		intron_variant		4		P1
NREP-AS1	ENST00000508389.1	n.82+1653G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81418 AN: 151726 Hom.: 22955 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.537 AC: 81483 AN: 151842 Hom.: 22977 Cov.: 32 AF XY: 0.544 AC XY: 40340 AN XY: 74162

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.511

Alfa AF: 0.408 Hom.: 1473

Bravo AF: 0.545

Asia WGS AF: 0.613 AC: 2131 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.56
Dann	Benign	0.33

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: rs6881837; hg19: chr5-111277484;