NM_080723.5:c.-9-1075T>C

Variant names:

• chr6-24133244-T-C
• rs12210008
• NM_080723.5:c.-9-1075T>C

Variant summary

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

The NM_080723.5(NRSN1):​c.-9-1075T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 152,260 control chromosomes in the GnomAD database, including 547 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 0.072 (547 hom., cov: 32)
• Consequence: NRSN1 NM_080723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080723.5. 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
	NRSN1	NM_080723.5	MANE Select	c.-9-1075T>C		intron	N/A	NP_542454.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRSN1	ENST00000378491.9	TSL:1 MANE Select	c.-9-1075T>C		intron	N/A	ENSP00000367752.4	Q8IZ57
	NRSN1	ENST00000378478.5	TSL:1	c.-9-1075T>C		intron	N/A	ENSP00000367739.2	Q8IZ57
	NRSN1	ENST00000378477.2	TSL:1	c.-9-1075T>C		intron	N/A	ENSP00000367738.2	Q5VTS0

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11033 AN: 152142 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0724 AC: 11025 AN: 152260 Hom.: 547 Cov.: 32 AF XY: 0.0766 AC XY: 5702 AN XY: 74442

African (AFR) AF: 0.0162 AC: 674 AN: 41574

American (AMR) AF: 0.0957 AC: 1464 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.172 AC: 889 AN: 5176

South Asian (SAS) AF: 0.103 AC: 495 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1639 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5379 AN: 68010

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0751 Hom.: 1607

Bravo AF: 0.0663

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		0.40
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: rs12210008; hg19: chr6-24133472;