ENST00000440698.1:n.880-31576G>T

Variant names:

• chr2-52284656-G-T
• rs17042688
• ENST00000440698.1:n.880-31576G>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.880-31576G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,204 control chromosomes in the GnomAD database, including 915 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 0.082 (915 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.880-31576G>T		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.880-31576G>T		intron_variant	Intron 7 of 10	2

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12465 AN: 152086 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0821 AC: 12499 AN: 152204 Hom.: 915 Cov.: 32 AF XY: 0.0824 AC XY: 6134 AN XY: 74408

African (AFR) AF: 0.190 AC: 7890 AN: 41510

American (AMR) AF: 0.0834 AC: 1275 AN: 15286

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

East Asian (EAS) AF: 0.112 AC: 579 AN: 5176

South Asian (SAS) AF: 0.0649 AC: 313 AN: 4822

European-Finnish (FIN) AF: 0.0412 AC: 437 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1736 AN: 68008

Other (OTH) AF: 0.0723 AC: 153 AN: 2116

Alfa AF: 0.0491 Hom.: 728

Bravo AF: 0.0897

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs17042688; hg19: chr2-52511794;