chr2-51821024-G-C

Variant names:

• chr2-51821024-G-C
• rs1017418
• ENST00000440698.1:n.840-40425G>C

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.840-40425G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,950 control chromosomes in the GnomAD database, including 22,296 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 0.53 (22296 hom., cov: 31)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.840-40425G>C		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.840-40425G>C		intron_variant	Intron 6 of 10	2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80071 AN: 151832 Hom.: 22260 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.528 AC: 80172 AN: 151950 Hom.: 22296 Cov.: 31 AF XY: 0.534 AC XY: 39658 AN XY: 74254

African (AFR) AF: 0.670 AC: 27739 AN: 41432

American (AMR) AF: 0.577 AC: 8796 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1406 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3640 AN: 5162

South Asian (SAS) AF: 0.555 AC: 2677 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5308 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29149 AN: 67942

Other (OTH) AF: 0.490 AC: 1034 AN: 2110

Alfa AF: 0.301 Hom.: 679

Bravo AF: 0.539

Asia WGS AF: 0.645 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.72
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1017418; hg19: chr2-52048162;