6-24141692-G-A

Variant names:

• chr6-24141692-G-A
• rs10946675
• NM_080723.5:c.190-3856G>A

Variant summary

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

The NM_080723.5(NRSN1):​c.190-3856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,098 control chromosomes in the GnomAD database, including 15,778 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 0.42 (15778 hom., cov: 33)
• Consequence: NRSN1 NM_080723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRSN1	NM_080723.5	c.190-3856G>A		intron_variant	Intron 3 of 3	ENST00000378491.9	NP_542454.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRSN1	ENST00000378491.9	c.190-3856G>A		intron_variant	Intron 3 of 3	1	NM_080723.5	ENSP00000367752.4

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64611 AN: 151978 Hom.: 15773 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 64615 AN: 152098 Hom.: 15778 Cov.: 33 AF XY: 0.431 AC XY: 32024 AN XY: 74340

African (AFR) AF: 0.189 AC: 7826 AN: 41514

American (AMR) AF: 0.469 AC: 7152 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1478 AN: 5172

South Asian (SAS) AF: 0.407 AC: 1963 AN: 4822

European-Finnish (FIN) AF: 0.656 AC: 6927 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36075 AN: 67986

Other (OTH) AF: 0.427 AC: 904 AN: 2116

Alfa AF: 0.492 Hom.: 81550

Bravo AF: 0.399

Asia WGS AF: 0.310 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		0.76
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: rs10946675; hg19: chr6-24141920;