2-51483165-T-C

Variant names:

• chr2-51483165-T-C
• rs1919417
• ENST00000440698.1:n.695-44437T>C

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.695-44437T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,986 control chromosomes in the GnomAD database, including 9,975 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 0.34 (9975 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 1 publications found

Genes affected

NRXN1-DT (HGNC:52686): (NRXN1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440698.1. 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
	NRXN1-DT	NR_135237.1		n.695-44437T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.695-44437T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51308 AN: 151868 Hom.: 9927 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.338 AC: 51422 AN: 151986 Hom.: 9975 Cov.: 32 AF XY: 0.347 AC XY: 25750 AN XY: 74250

African (AFR) AF: 0.485 AC: 20106 AN: 41436

American (AMR) AF: 0.373 AC: 5692 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3064 AN: 5122

South Asian (SAS) AF: 0.433 AC: 2079 AN: 4804

European-Finnish (FIN) AF: 0.322 AC: 3407 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15523 AN: 67990

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.280 Hom.: 900

Bravo AF: 0.346

Asia WGS AF: 0.549 AC: 1903 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		-0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1919417;

hg19: chr2-51710303;