ENST00000440698.1:n.515-42803C>T

Variant names:

• chr2-51285586-C-T
• rs4971738
• ENST00000440698.1:n.515-42803C>T

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.515-42803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,762 control chromosomes in the GnomAD database, including 2,195 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 0.16 (2195 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.515-42803C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.515-42803C>T		intron_variant	Intron 2 of 10	2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23807 AN: 151640 Hom.: 2189 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.157 AC: 23849 AN: 151762 Hom.: 2195 Cov.: 32 AF XY: 0.164 AC XY: 12184 AN XY: 74172

African (AFR) AF: 0.172 AC: 7122 AN: 41428

American (AMR) AF: 0.192 AC: 2924 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1972 AN: 5164

South Asian (SAS) AF: 0.252 AC: 1213 AN: 4816

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10560

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7356 AN: 67788

Other (OTH) AF: 0.158 AC: 333 AN: 2108

Alfa AF: 0.146 Hom.: 320

Bravo AF: 0.156

Asia WGS AF: 0.351 AC: 1215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4971738; hg19: chr2-51512724;