2-51730805-C-G

Variant names:

• chr2-51730805-C-G
• rs10208467
• ENST00000440698.1:n.754-31284C>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.754-31284C>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 152,102 control chromosomes in the GnomAD database, including 45,885 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 (45885 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-31284C>G		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.754-31284C>G		intron_variant	Intron 5 of 10	2
NRXN1-DT	ENST00000843923.1	n.46-31284C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117764 AN: 151984 Hom.: 45866 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.775 AC: 117836 AN: 152102 Hom.: 45885 Cov.: 32 AF XY: 0.779 AC XY: 57914 AN XY: 74326

African (AFR) AF: 0.806 AC: 33464 AN: 41522

American (AMR) AF: 0.725 AC: 11062 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2626 AN: 3468

East Asian (EAS) AF: 0.993 AC: 5134 AN: 5172

South Asian (SAS) AF: 0.803 AC: 3874 AN: 4822

European-Finnish (FIN) AF: 0.765 AC: 8095 AN: 10578

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51057 AN: 67980

Other (OTH) AF: 0.774 AC: 1632 AN: 2108

Alfa AF: 0.724 Hom.: 2491

Bravo AF: 0.769

Asia WGS AF: 0.892 AC: 3102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.049
DANN	Benign	0.60
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10208467; hg19: chr2-51957943;