rs11889082

Positions:

• chr2-51044980-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440698.1(ENSG00000231918):​n.417-7377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 152,256 control chromosomes in the GnomAD database, including 851 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 0.10 (851 hom., cov: 33)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

ENSG00000231918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.417-7377A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.417-7377A>G		intron_variant		2
NRXN1	ENST00000635126.1	n.320-11846T>C		intron_variant		5
NRXN1	ENST00000635310.1	n.426-15786T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15181 AN: 152138 Hom.: 846 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0999 AC: 15207 AN: 152256 Hom.: 851 Cov.: 33 AF XY: 0.101 AC XY: 7496 AN XY: 74444

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0714

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0903 Hom.: 123

Bravo AF: 0.0998

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11889082; hg19: chr2-51272118;