6-24135616-G-C

Variant names:

• chr6-24135616-G-C
• rs12208318
• NM_080723.5:c.189+1100G>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.189+1100G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0717 in 152,278 control chromosomes in the GnomAD database, including 543 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 (543 hom., cov: 32)
• Consequence: NRSN1 NM_080723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRSN1	NM_080723.5	MANE Select	c.189+1100G>C		intron	N/A	NP_542454.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRSN1	ENST00000378491.9	TSL:1 MANE Select	c.189+1100G>C		intron	N/A	ENSP00000367752.4
	NRSN1	ENST00000378478.5	TSL:1	c.189+1100G>C		intron	N/A	ENSP00000367739.2
	NRSN1	ENST00000378477.2	TSL:1	c.189+1100G>C		intron	N/A	ENSP00000367738.2

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10923 AN: 152160 Hom.: 545 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0717 AC: 10916 AN: 152278 Hom.: 543 Cov.: 32 AF XY: 0.0757 AC XY: 5639 AN XY: 74454

African (AFR) AF: 0.0160 AC: 664 AN: 41564

American (AMR) AF: 0.0954 AC: 1460 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3470

East Asian (EAS) AF: 0.170 AC: 879 AN: 5178

South Asian (SAS) AF: 0.102 AC: 493 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1616 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0784 AC: 5329 AN: 68010

Other (OTH) AF: 0.0782 AC: 165 AN: 2110

Alfa AF: 0.0698 Hom.: 56

Bravo AF: 0.0658

Asia WGS AF: 0.132 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		0.13
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: rs12208318; hg19: chr6-24135844;