chr2-51823161-A-G

Variant names:

• chr2-51823161-A-G
• rs983511
• ENST00000440698.1:n.840-38288A>G

Variant summary

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

The ENST00000440698.1(NRXN1-DT):​n.840-38288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,212 control chromosomes in the GnomAD database, including 58,242 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 0.87 (58242 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.840-38288A>G		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRXN1-DT	ENST00000440698.1	n.840-38288A>G		intron_variant	Intron 6 of 10	2

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132657 AN: 152094 Hom.: 58186 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.872 AC: 132775 AN: 152212 Hom.: 58242 Cov.: 32 AF XY: 0.876 AC XY: 65155 AN XY: 74394

African (AFR) AF: 0.959 AC: 39825 AN: 41546

American (AMR) AF: 0.870 AC: 13303 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5157 AN: 5168

South Asian (SAS) AF: 0.857 AC: 4134 AN: 4822

European-Finnish (FIN) AF: 0.860 AC: 9111 AN: 10592

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55679 AN: 68006

Other (OTH) AF: 0.841 AC: 1773 AN: 2108

Alfa AF: 0.852 Hom.: 7158

Bravo AF: 0.878

Asia WGS AF: 0.944 AC: 3279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.74
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs983511; hg19: chr2-52050299;