2-52308269-T-G

Variant names:

• chr2-52308269-T-G
• rs12475021
• ENST00000440698.1:n.880-7963T>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.880-7963T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,166 control chromosomes in the GnomAD database, including 795 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 0.078 (795 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.880-7963T>G		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.880-7963T>G		intron_variant	Intron 7 of 10	2

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11789 AN: 152046 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.0655

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

GnomAD4 genome AF: 0.0777 AC: 11817 AN: 152166 Hom.: 795 Cov.: 32 AF XY: 0.0780 AC XY: 5806 AN XY: 74404

African (AFR) AF: 0.175 AC: 7265 AN: 41516

American (AMR) AF: 0.0811 AC: 1240 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5174

South Asian (SAS) AF: 0.0649 AC: 313 AN: 4826

European-Finnish (FIN) AF: 0.0410 AC: 435 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0253 AC: 1721 AN: 67972

Other (OTH) AF: 0.0648 AC: 137 AN: 2114

Alfa AF: 0.0375 Hom.: 330

Bravo AF: 0.0845

Asia WGS AF: 0.0970 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs12475021; hg19: chr2-52535407;