rs10495997

Variant names:

• chr2-51524392-C-G
• rs10495997
• ENST00000440698.1:n.695-3210C>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.695-3210C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,206 control chromosomes in the GnomAD database, including 233 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 0.036 (233 hom., cov: 32)
• Consequence: NRXN1-DT ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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.695-3210C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRXN1-DT	ENST00000440698.1	TSL:2	n.695-3210C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5411 AN: 152088 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.00720

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0355 AC: 5407 AN: 152206 Hom.: 233 Cov.: 32 AF XY: 0.0399 AC XY: 2971 AN XY: 74432

African (AFR) AF: 0.00717 AC: 298 AN: 41538

American (AMR) AF: 0.0629 AC: 961 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1040 AN: 5148

South Asian (SAS) AF: 0.0682 AC: 329 AN: 4826

European-Finnish (FIN) AF: 0.0683 AC: 724 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1942 AN: 68010

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0257 Hom.: 8

Bravo AF: 0.0346

Asia WGS AF: 0.121 AC: 418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-0.14
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: rs10495997; hg19: chr2-51751530;