Genetic Variant NRSN1:c.*1309A>T (chr6-24147255-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_080723.5(NRSN1):c.*1309A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Failed GnomAD Quality Control

Consequence

NRSN1
NM_080723.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

6 publications found

Variant links:

Genes affected

NRSN1 (HGNC:17881): (neurensin 1) Predicted to be involved in nervous system development. Predicted to be located in cytoplasmic vesicle and growth cone. Predicted to be active in neuron projection; neuronal cell body; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

NRSN1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRSN1	NM_080723.5 link	c.*1309A>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000378491.9	NP_542454.3	Q8IZ57

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NRSN1	ENST00000378491.9 link	c.*1309A>T	3_prime_UTR_variant	Exon 4 of 4	1	NM_080723.5	ENSP00000367752.4	Q8IZ57
NRSN1	ENST00000378478.5 link	c.*1309A>T	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000367739.2	Q8IZ57
NRSN1	ENST00000468195.2 link	n.257-7516A>T	intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

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American (AMR)

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Ashkenazi Jewish (ASJ)

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East Asian (EAS)

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South Asian (SAS)

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European-Finnish (FIN)

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Middle Eastern (MID)

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European-Non Finnish (NFE)

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Other (OTH)

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GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

27189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.12

(source)

DANN

Benign

0.68

PhyloP100

-1.6

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over