chr2-51732120-T-C

Variant names:

• chr2-51732120-T-C
• rs1533428
• ENST00000440698.1:n.754-29969T>C

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.754-29969T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,044 control chromosomes in the GnomAD database, including 35,691 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 0.68 (35691 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-29969T>C		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.754-29969T>C		intron_variant	Intron 5 of 10	2
NRXN1-DT	ENST00000843923.1	n.46-29969T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103714 AN: 151926 Hom.: 35669 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.682 AC: 103770 AN: 152044 Hom.: 35691 Cov.: 32 AF XY: 0.684 AC XY: 50853 AN XY: 74314

African (AFR) AF: 0.619 AC: 25673 AN: 41468

American (AMR) AF: 0.661 AC: 10089 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2571 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3165 AN: 5154

South Asian (SAS) AF: 0.677 AC: 3257 AN: 4814

European-Finnish (FIN) AF: 0.723 AC: 7634 AN: 10566

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49043 AN: 67988

Other (OTH) AF: 0.698 AC: 1474 AN: 2112

Alfa AF: 0.708 Hom.: 20587

Bravo AF: 0.672

Asia WGS AF: 0.636 AC: 2213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1533428; hg19: chr2-51959258;