2-51723186-C-T

Variant names:

• chr2-51723186-C-T
• rs10202118
• ENST00000440698.1:n.754-38903C>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.754-38903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 151,578 control chromosomes in the GnomAD database, including 35,259 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 0.67 (35259 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.754-38903C>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.754-38903C>T		intron_variant	Intron 5 of 10	2
NRXN1-DT	ENST00000843923.1	n.45+36732C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101501 AN: 151460 Hom.: 35259 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.670 AC: 101514 AN: 151578 Hom.: 35259 Cov.: 31 AF XY: 0.673 AC XY: 49863 AN XY: 74102

African (AFR) AF: 0.467 AC: 19352 AN: 41398

American (AMR) AF: 0.740 AC: 11229 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2765 AN: 3466

East Asian (EAS) AF: 0.595 AC: 3069 AN: 5158

South Asian (SAS) AF: 0.730 AC: 3515 AN: 4818

European-Finnish (FIN) AF: 0.774 AC: 8167 AN: 10556

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51095 AN: 67698

Other (OTH) AF: 0.681 AC: 1431 AN: 2100

Alfa AF: 0.732 Hom.: 21110

Bravo AF: 0.659

Asia WGS AF: 0.626 AC: 2171 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10202118; hg19: chr2-51950324;