chr2-51644203-A-G

Variant names:

• chr2-51644203-A-G
• rs1516174
• ENST00000440698.1:n.753+116543A>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+116543A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 151,394 control chromosomes in the GnomAD database, including 45,826 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 0.77 (45826 hom., cov: 30)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 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+116543A>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+116543A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117236 AN: 151276 Hom.: 45818 Cov.: 30

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.775 AC: 117277 AN: 151394 Hom.: 45826 Cov.: 30 AF XY: 0.777 AC XY: 57459 AN XY: 73910

African (AFR) AF: 0.674 AC: 27821 AN: 41308

American (AMR) AF: 0.828 AC: 12539 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3048 AN: 3462

East Asian (EAS) AF: 0.734 AC: 3738 AN: 5096

South Asian (SAS) AF: 0.809 AC: 3886 AN: 4806

European-Finnish (FIN) AF: 0.818 AC: 8666 AN: 10588

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 54970 AN: 67684

Other (OTH) AF: 0.771 AC: 1617 AN: 2098

Alfa AF: 0.806 Hom.: 37665

Bravo AF: 0.772

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.79
DANN	Benign	0.54
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1516174; hg19: chr2-51871341;