rs4314028

Variant names:

• chr2-51909527-T-C
• rs4314028
• ENST00000440698.1:n.879+48039T>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.879+48039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,986 control chromosomes in the GnomAD database, including 3,652 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 0.21 (3652 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.879+48039T>C		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.879+48039T>C		intron_variant	Intron 7 of 10	2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31667 AN: 151870 Hom.: 3654 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.208 AC: 31688 AN: 151986 Hom.: 3652 Cov.: 32 AF XY: 0.208 AC XY: 15460 AN XY: 74284

African (AFR) AF: 0.135 AC: 5616 AN: 41504

American (AMR) AF: 0.204 AC: 3111 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.105 AC: 540 AN: 5164

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4822

European-Finnish (FIN) AF: 0.204 AC: 2151 AN: 10556

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16693 AN: 67894

Other (OTH) AF: 0.245 AC: 515 AN: 2100

Alfa AF: 0.244 Hom.: 2857

Bravo AF: 0.202

Asia WGS AF: 0.209 AC: 724 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs4314028; hg19: chr2-52136665;