rs11125375

Variant names:

• chr2-51725011-G-A
• rs11125375
• ENST00000440698.1:n.754-37078G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-51725011-G-A
• chr2-51725011-G-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.754-37078G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,768 control chromosomes in the GnomAD database, including 28,866 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 0.61 (28866 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-37078G>A		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.754-37078G>A		intron_variant	Intron 5 of 10	2
NRXN1-DT	ENST00000843923.1	n.46-37078G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92383 AN: 151650 Hom.: 28871 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.609 AC: 92386 AN: 151768 Hom.: 28866 Cov.: 31 AF XY: 0.613 AC XY: 45430 AN XY: 74162

African (AFR) AF: 0.463 AC: 19159 AN: 41396

American (AMR) AF: 0.616 AC: 9361 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2961 AN: 5148

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4820

European-Finnish (FIN) AF: 0.692 AC: 7306 AN: 10554

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46079 AN: 67882

Other (OTH) AF: 0.614 AC: 1290 AN: 2100

Alfa AF: 0.653 Hom.: 17623

Bravo AF: 0.594

Asia WGS AF: 0.573 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.62
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11125375; hg19: chr2-51952149;