chr2-51759851-T-C

Position:

• chr2-51759851-T-C

Variant summary

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

The ENST00000440698.1(ENSG00000231918):​n.754-2238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 150,344 control chromosomes in the GnomAD database, including 17,364 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 0.45 (17364 hom., cov: 32)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

ENSG00000231918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-2238T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.754-2238T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 67476 AN: 150228 Hom.: 17287 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.450 AC: 67620 AN: 150344 Hom.: 17364 Cov.: 32 AF XY: 0.455 AC XY: 33433 AN XY: 73502

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.431

Alfa AF: 0.231 Hom.: 506

Bravo AF: 0.471

Asia WGS AF: 0.614 AC: 2130 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2176221; hg19: chr2-51986989;