rs9356928

chr6-24131107-G-Achr6-24131107-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080723.5(NRSN1):c.-10+2907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,074 control chromosomes in the GnomAD database, including 26,425 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 0.57 (26425 hom., cov: 32)
• Consequence: NRSN1 NM_080723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NRSN1	NM_080723.5	c.-10+2907G>A		intron_variant		ENST00000378491.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRSN1	ENST00000378491.9	c.-10+2907G>A		intron_variant		1	NM_080723.5	P1
NRSN1	ENST00000378477.2	c.-10+2907G>A		intron_variant		1
NRSN1	ENST00000378478.5	c.-10+2907G>A		intron_variant		1		P1
NRSN1	ENST00000468195.2	n.58+2907G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86509 AN: 151956 Hom.: 26371 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.570 AC: 86621 AN: 152074 Hom.: 26425 Cov.: 32 AF XY: 0.567 AC XY: 42162 AN XY: 74326

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.574

Alfa AF: 0.483 Hom.: 6392

Bravo AF: 0.588

Asia WGS AF: 0.709 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.51

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: rs9356928; hg19: chr6-24131335;