2-51040002-C-T

Position:

• chr2-51040002-C-T

Variant summary

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

The NR_135237.1(NRXN1-DT):​n.416+6986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,092 control chromosomes in the GnomAD database, including 2,549 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 0.15 (2549 hom., cov: 33)
• Consequence: NRXN1-DT NR_135237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

ENSG00000231918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.416+6986C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.416+6986C>T		intron_variant		2
NRXN1	ENST00000635126.1	n.320-6868G>A		intron_variant		5
NRXN1	ENST00000635310.1	n.426-10808G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23065 AN: 151974 Hom.: 2539 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.152 AC: 23105 AN: 152092 Hom.: 2549 Cov.: 33 AF XY: 0.150 AC XY: 11160 AN XY: 74350

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0852

Gnomad4 OTH AF: 0.159

Alfa AF: 0.108 Hom.: 536

Bravo AF: 0.160

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193411; hg19: chr2-51267140;