rs12994401

Variant names:

• chr2-51845108-C-T
• rs12994401
• ENST00000440698.1:n.840-16341C>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.840-16341C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,076 control chromosomes in the GnomAD database, including 2,891 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 0.18 (2891 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 12 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440698.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	NR_135237.1		n.840-16341C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.840-16341C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28038 AN: 151958 Hom.: 2889 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.184 AC: 28049 AN: 152076 Hom.: 2891 Cov.: 32 AF XY: 0.189 AC XY: 14056 AN XY: 74358

African (AFR) AF: 0.0861 AC: 3574 AN: 41492

American (AMR) AF: 0.214 AC: 3259 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1767 AN: 5160

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4828

European-Finnish (FIN) AF: 0.286 AC: 3027 AN: 10576

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13919 AN: 67972

Other (OTH) AF: 0.197 AC: 417 AN: 2116

Alfa AF: 0.195 Hom.: 5064

Bravo AF: 0.175

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12994401;

hg19: chr2-52072246;