2-51509856-C-T

Position:

• chr2-51509856-C-T

Variant summary

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

The ENST00000440698.1(ENSG00000231918):​n.695-17746C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,036 control chromosomes in the GnomAD database, including 3,724 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 0.21 (3724 hom., cov: 31)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.695-17746C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.695-17746C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31675 AN: 151918 Hom.: 3694 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.209 AC: 31758 AN: 152036 Hom.: 3724 Cov.: 31 AF XY: 0.215 AC XY: 15945 AN XY: 74310

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.218

Alfa AF: 0.186 Hom.: 4533

Bravo AF: 0.210

Asia WGS AF: 0.417 AC: 1448 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	0.086
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406428; hg19: chr2-51736994;