ENST00000440698.1:n.880-101588C>G

Variant names:

• chr2-52214644-C-G
• rs1922185
• ENST00000440698.1:n.880-101588C>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.880-101588C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,868 control chromosomes in the GnomAD database, including 10,203 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 0.36 (10203 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 0 publications found

Genes affected

NRXN1-DT (HGNC:52686): (NRXN1 divergent transcript)

ENSG00000302235 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.880-101588C>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.880-101588C>G		intron_variant	Intron 7 of 10	2
ENSG00000302235	ENST00000785119.1	n.214-26292G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54111 AN: 151750 Hom.: 10194 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.356 AC: 54141 AN: 151868 Hom.: 10203 Cov.: 31 AF XY: 0.357 AC XY: 26507 AN XY: 74222

African (AFR) AF: 0.233 AC: 9641 AN: 41414

American (AMR) AF: 0.492 AC: 7495 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1527 AN: 5140

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4812

European-Finnish (FIN) AF: 0.424 AC: 4474 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26665 AN: 67940

Other (OTH) AF: 0.374 AC: 788 AN: 2106

Alfa AF: 0.371 Hom.: 1354

Bravo AF: 0.361

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1922185; hg19: chr2-52441782;