rs12210008

Positions:

• chr6-24133244-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRSN1	NM_080723.5	c.-9-1075T>C		intron_variant		ENST00000378491.9	NP_542454.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRSN1	ENST00000378491.9	c.-9-1075T>C		intron_variant		1	NM_080723.5	ENSP00000367752.4
NRSN1	ENST00000378478.5	c.-9-1075T>C		intron_variant		1		ENSP00000367739.2
NRSN1	ENST00000378477.2	c.-9-1075T>C		intron_variant		1		ENSP00000367738.2
NRSN1	ENST00000468195.2	n.59-1075T>C		intron_variant		5

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

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.0714

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0776 Hom.: 1056

Bravo AF: 0.0663

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.75

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: rs12210008; hg19: chr6-24133472;