NM_080723.5:c.*1309A>G

Variant names:

• chr6-24147255-A-G
• rs1053047
• NM_080723.5:c.*1309A>G

Variant summary

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

The NM_080723.5(NRSN1):​c.*1309A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,082 control chromosomes in the GnomAD database, including 15,907 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 0.43 (15907 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NRSN1 NM_080723.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 6 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64884 AN: 151964 Hom.: 15902 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.433

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.427 AC: 64888 AN: 152082 Hom.: 15907 Cov.: 32 AF XY: 0.433 AC XY: 32195 AN XY: 74326

African (AFR) AF: 0.189 AC: 7846 AN: 41500

American (AMR) AF: 0.470 AC: 7189 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1582 AN: 3464

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5164

South Asian (SAS) AF: 0.409 AC: 1969 AN: 4818

European-Finnish (FIN) AF: 0.660 AC: 6978 AN: 10568

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36200 AN: 67962

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.488 Hom.: 27189

Bravo AF: 0.400

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.15
DANN	Benign	0.75
PhyloP100		-1.6
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: rs1053047; hg19: chr6-24147483;