2-51462538-T-G

Variant names:

• chr2-51462538-T-G
• rs991902
• ENST00000440698.1:n.695-65064T>G

Variant summary

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

The ENST00000440698.1(ENSG00000231918):​n.695-65064T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,124 control chromosomes in the GnomAD database, including 959 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 0.10 (959 hom., cov: 32)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.695-65064T>G		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.695-65064T>G		intron_variant	Intron 4 of 10	2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15223 AN: 152006 Hom.: 948 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.100 AC: 15273 AN: 152124 Hom.: 959 Cov.: 32 AF XY: 0.108 AC XY: 8011 AN XY: 74374

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0455 Hom.: 34

Bravo AF: 0.0957

Asia WGS AF: 0.239 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991902; hg19: chr2-51689676;