2-51644383-A-G

Variant names:

• chr2-51644383-A-G
• rs925801
• ENST00000440698.1:n.753+116723A>G

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.753+116723A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 151,460 control chromosomes in the GnomAD database, including 53,518 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 0.84 (53518 hom., cov: 30)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.843 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.753+116723A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.753+116723A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127135 AN: 151344 Hom.: 53497 Cov.: 30

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.840 AC: 127199 AN: 151460 Hom.: 53518 Cov.: 30 AF XY: 0.841 AC XY: 62172 AN XY: 73948

African (AFR) AF: 0.839 AC: 34738 AN: 41392

American (AMR) AF: 0.855 AC: 12965 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3098 AN: 3460

East Asian (EAS) AF: 0.732 AC: 3726 AN: 5092

South Asian (SAS) AF: 0.843 AC: 4062 AN: 4816

European-Finnish (FIN) AF: 0.848 AC: 8960 AN: 10572

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 56841 AN: 67664

Other (OTH) AF: 0.830 AC: 1740 AN: 2096

Alfa AF: 0.840 Hom.: 19801

Bravo AF: 0.841

Asia WGS AF: 0.784 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.35

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: rs925801;

hg19: chr2-51871521;