chr2-51588242-A-G

Variant names:

• chr2-51588242-A-G
• rs12478948
• ENST00000440698.1:n.753+60582A>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+60582A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,446 control chromosomes in the GnomAD database, including 22,315 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 0.54 (22315 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 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+60582A>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+60582A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81566 AN: 151326 Hom.: 22276 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.539 AC: 81658 AN: 151446 Hom.: 22315 Cov.: 31 AF XY: 0.543 AC XY: 40180 AN XY: 73976

African (AFR) AF: 0.567 AC: 23462 AN: 41366

American (AMR) AF: 0.629 AC: 9582 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1836 AN: 3462

East Asian (EAS) AF: 0.562 AC: 2893 AN: 5150

South Asian (SAS) AF: 0.659 AC: 3176 AN: 4820

European-Finnish (FIN) AF: 0.505 AC: 5304 AN: 10508

Middle Eastern (MID) AF: 0.604 AC: 174 AN: 288

European-Non Finnish (NFE) AF: 0.497 AC: 33594 AN: 67614

Other (OTH) AF: 0.549 AC: 1156 AN: 2104

Alfa AF: 0.515 Hom.: 67906

Bravo AF: 0.550

Asia WGS AF: 0.582 AC: 2013 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.50
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12478948; hg19: chr2-51815380;