2-52214644-C-G

Position:

• chr2-52214644-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440698.1(ENSG00000231918):​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: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.880-101588C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.880-101588C>G		intron_variant		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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.374

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1922185; hg19: chr2-52441782;