rs1206397

Variant names:

• chr2-51440601-C-A
• rs1206397
• ENST00000440698.1:n.694+62428C>A

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.694+62428C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 151,840 control chromosomes in the GnomAD database, including 113 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 0.032 (113 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.694+62428C>A		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.694+62428C>A		intron_variant	Intron 4 of 10	2

Frequencies

GnomAD3 genomes AF: 0.0325 AC: 4927 AN: 151722 Hom.: 112 Cov.: 31

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0467

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

GnomAD4 genome AF: 0.0325 AC: 4930 AN: 151840 Hom.: 113 Cov.: 31 AF XY: 0.0327 AC XY: 2425 AN XY: 74176

African (AFR) AF: 0.0346 AC: 1436 AN: 41450

American (AMR) AF: 0.0219 AC: 334 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.135 AC: 692 AN: 5138

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4816

European-Finnish (FIN) AF: 0.0230 AC: 242 AN: 10524

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1806 AN: 67894

Other (OTH) AF: 0.0458 AC: 96 AN: 2098

Alfa AF: 0.0289 Hom.: 63

Bravo AF: 0.0340

Asia WGS AF: 0.0770 AC: 266 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.17
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1206397; hg19: chr2-51667739;