rs6798572

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001365925.2(NLGN1):​c.707-154412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,184 control chromosomes in the GnomAD database, including 1,541 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 0.13 ( 1541 hom., cov: 32)

Consequence

NLGN1
NM_001365925.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65
Variant links:
Genes affected
NLGN1 (HGNC:14291): (neuroligin 1) This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NLGN1NM_001365925.2 linkuse as main transcriptc.707-154412A>G intron_variant ENST00000695368.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NLGN1ENST00000695368.1 linkuse as main transcriptc.707-154412A>G intron_variant NM_001365925.2 A1
NLGN1ENST00000361589.8 linkuse as main transcriptc.647-154412A>G intron_variant 1 P2Q8N2Q7-2
NLGN1ENST00000415045.2 linkuse as main transcriptc.767-154412A>G intron_variant 1 Q8N2Q7-3
NLGN1ENST00000457714.5 linkuse as main transcriptc.647-154412A>G intron_variant 1 P2Q8N2Q7-2

Frequencies

GnomAD3 genomes
AF:
0.133
AC:
20163
AN:
152062
Hom.:
1543
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.159
Gnomad AMR
AF:
0.0802
Gnomad ASJ
AF:
0.0864
Gnomad EAS
AF:
0.179
Gnomad SAS
AF:
0.0882
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.121
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.133
AC:
20186
AN:
152184
Hom.:
1541
Cov.:
32
AF XY:
0.131
AC XY:
9734
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.0801
Gnomad4 ASJ
AF:
0.0864
Gnomad4 EAS
AF:
0.179
Gnomad4 SAS
AF:
0.0887
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.110
Hom.:
499
Bravo
AF:
0.134
Asia WGS
AF:
0.124
AC:
432
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.15
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6798572; hg19: chr3-173838693; API