rs173896

Variant names:

• chr5-111771418-T-A
• rs173896
• NM_001142475.2:c.136-35911A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-111771418-T-A
• chr5-111771418-T-C

Variant summary

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

The NM_001142475.2(NREP):​c.136-35911A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 143,016 control chromosomes in the GnomAD database, including 469 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 0.070 (469 hom., cov: 30)
• Consequence: NREP NM_001142475.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 5 publications found

Genes affected

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142475.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NREP	NM_001142475.2		c.136-35911A>T		intron	N/A	NP_001135947.1	Q16612-2
	NREP	NM_001142474.2		c.106-35911A>T		intron	N/A	NP_001135946.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NREP	ENST00000395634.7	TSL:2	c.136-35911A>T		intron	N/A	ENSP00000378996.3	Q16612-2
	NREP	ENST00000450761.6	TSL:4	c.-58-15588A>T		intron	N/A	ENSP00000416617.2	Q16612-1

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10009 AN: 142898 Hom.: 470 Cov.: 30

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.0324

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0691

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0700 AC: 10010 AN: 143016 Hom.: 469 Cov.: 30 AF XY: 0.0731 AC XY: 5076 AN XY: 69398

African (AFR) AF: 0.0192 AC: 697 AN: 36320

American (AMR) AF: 0.0674 AC: 939 AN: 13934

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 367 AN: 3434

East Asian (EAS) AF: 0.235 AC: 1161 AN: 4950

South Asian (SAS) AF: 0.151 AC: 686 AN: 4556

European-Finnish (FIN) AF: 0.0649 AC: 639 AN: 9850

Middle Eastern (MID) AF: 0.0599 AC: 17 AN: 284

European-Non Finnish (NFE) AF: 0.0798 AC: 5330 AN: 66824

Other (OTH) AF: 0.0737 AC: 145 AN: 1968

Alfa AF: 0.0604 Hom.: 41

Bravo AF: 0.0630

Asia WGS AF: 0.155 AC: 540 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.83
PhyloP100		0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs173896; hg19: chr5-111107115;