chr2-51700904-G-T

Variant names:

• chr2-51700904-G-T
• rs1028145
• ENST00000440698.1:n.754-61185G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440698.1(NRXN1-DT):​n.754-61185G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 151,692 control chromosomes in the GnomAD database, including 58,302 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 0.88 (58302 hom., cov: 29)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 3 publications found

Genes affected

NRXN1-DT (HGNC:52686): (NRXN1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-61185G>T		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.754-61185G>T		intron_variant	Intron 5 of 10	2
NRXN1-DT	ENST00000843923.1	n.45+14450G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.876 AC: 132785 AN: 151580 Hom.: 58269 Cov.: 29

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.876 AC: 132869 AN: 151692 Hom.: 58302 Cov.: 29 AF XY: 0.878 AC XY: 65108 AN XY: 74132

African (AFR) AF: 0.875 AC: 36254 AN: 41426

American (AMR) AF: 0.894 AC: 13625 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3078 AN: 3466

East Asian (EAS) AF: 0.980 AC: 5064 AN: 5168

South Asian (SAS) AF: 0.904 AC: 4355 AN: 4816

European-Finnish (FIN) AF: 0.901 AC: 9479 AN: 10518

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.858 AC: 58109 AN: 67752

Other (OTH) AF: 0.865 AC: 1823 AN: 2108

Alfa AF: 0.862 Hom.: 88836

Bravo AF: 0.876

Asia WGS AF: 0.924 AC: 3215 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	1.5
DANN	Benign	0.42
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1028145; hg19: chr2-51928042;