2-52187585-A-G

Variant names:

• chr2-52187585-A-G
• rs1922197
• ENST00000440698.1:n.880-128647A>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.880-128647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,130 control chromosomes in the GnomAD database, including 3,502 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 0.15 (3502 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 3 publications found

Genes affected

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

ENSG00000302235 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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.880-128647A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.880-128647A>G		intron	N/A
	ENSG00000302235	ENST00000785119.1		n.288+693T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22132 AN: 152012 Hom.: 3484 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.146 AC: 22206 AN: 152130 Hom.: 3502 Cov.: 32 AF XY: 0.148 AC XY: 10998 AN XY: 74392

African (AFR) AF: 0.360 AC: 14925 AN: 41462

American (AMR) AF: 0.0781 AC: 1193 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2399 AN: 5160

South Asian (SAS) AF: 0.181 AC: 874 AN: 4822

European-Finnish (FIN) AF: 0.0414 AC: 440 AN: 10620

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1920 AN: 68008

Other (OTH) AF: 0.134 AC: 282 AN: 2104

Alfa AF: 0.0601 Hom.: 475

Bravo AF: 0.160

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.90
PhyloP100		0.54

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: rs1922197;

hg19: chr2-52414723;