2-51699459-CAATGCCCCACTTAATGCAGGTTGAGAAATAAGTGAAACTATGACATGGAAAAATATTACAATAAGCGAAAAATATTACAATAAAGGAAAAAATAATGGAAGAATATCAGTATTTGATGCTATTATACGTGACCATATTGTTTAGCAAACTACTTCAAAAATGAAATTAGGAATTTCAGAGAATCATTTTATTCTCATATCAGAATGCTTGGAAAAGTGAGGGCTAAATGTATTTGTTATTTGACTGTGTACATTATGCCCATGGAATAGCATTTTGGAAGACCCAACATTAAGCTAGCTTTACATA-C

Variant names:

• chr2-51699459-CAATGCCCCACTTAATGCAGGTTGAGAAATAAGTGAAACTATGACATGGAAAAATATTACAATAAGCGAAAAATATTACAATAAAGGAAAAAATAATGGAAGAATATCAGTATTTGATGCTATTATACGTGACCATATTGTTTAGCAAACTACTTCAAAAATGAAATTAGGAATTTCAGAGAATCATTTTATTCTCATATCAGAATGCTTGGAAAAGTGAGGGCTAAATGTATTTGTTATTTGACTGTGTACATTATGCCCATGGAATAGCATTTTGGAAGACCCAACATTAAGCTAGCTTTACATA-C
• rs1553354646
• ENST00000440698.1:n.754-62629_754-62324del

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000440698.1(ENSG00000231918):​n.754-62629_754-62324del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 30)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: not provided no classification provided O:4
• Conservation: PhyloP100: 0.731

Genes affected

ENSG00000231918 (HGNC:52686): (NRXN1 divergent transcript)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-62628_754-62323del		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.754-62629_754-62324del		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Significance: not provided

Submissions summary: Other:4

Revision: no classification provided

Submissions by phenotype

Large for gestational age Other:1

-

Institute of Molecular and Cell Biology, University of Tartu

Significance: not provided

Review Status: no classification provided

Collection Method: case-control

- -

Gestational diabetes mellitus uncontrolled Other:1

-

Institute of Molecular and Cell Biology, University of Tartu

Significance: not provided

Review Status: no classification provided

Collection Method: case-control

- -

Normal pregnancy Other:1

-

Institute of Molecular and Cell Biology, University of Tartu

Significance: not provided

Review Status: no classification provided

Collection Method: case-control

- -

Preeclampsia Other:1

-

Institute of Molecular and Cell Biology, University of Tartu

Significance: not provided

Review Status: no classification provided

Collection Method: case-control

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553354646; hg19: chr2-51926597;