rs2839839

Variant names:

• chr2-51464346-A-C
• rs2839839
• ENST00000440698.1:n.695-63256A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-51464346-A-C
• chr2-51464346-A-G
• chr2-51464346-A-T

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.695-63256A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,102 control chromosomes in the GnomAD database, including 3,578 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 0.18 (3578 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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.695-63256A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.695-63256A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26896 AN: 151984 Hom.: 3542 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.0439

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.177 AC: 26986 AN: 152102 Hom.: 3578 Cov.: 32 AF XY: 0.188 AC XY: 14005 AN XY: 74372

African (AFR) AF: 0.282 AC: 11704 AN: 41492

American (AMR) AF: 0.227 AC: 3470 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0439 AC: 152 AN: 3462

East Asian (EAS) AF: 0.532 AC: 2749 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4814

European-Finnish (FIN) AF: 0.167 AC: 1769 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0747 AC: 5076 AN: 67990

Other (OTH) AF: 0.171 AC: 361 AN: 2114

Alfa AF: 0.146 Hom.: 410

Bravo AF: 0.186

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.068
DANN	Benign	0.65
PhyloP100		-0.71

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: rs2839839;

hg19: chr2-51691484;