Genetic Variant ENST00000440698.1:n.616-24677A>G (chr2-51353418-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000440698.1(NRXN1-DT):n.616-24677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 152,234 control chromosomes in the GnomAD database, including 365 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 0.049 ( 365 hom., cov: 32)

Consequence

NRXN1-DT
ENST00000440698.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574

Publications

1 publications found

Variant links:

Genes affected

NRXN1-DT (HGNC:52686): (NRXN1 divergent transcript)

NRXN1-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1 link	n.616-24677A>G		intron_variant	Intron 3 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NRXN1-DT	ENST00000440698.1 link	n.616-24677A>G	intron_variant	Intron 3 of 10	2
NRXN1-DT	ENST00000779111.1 link	n.194-24677A>G	intron_variant	Intron 2 of 3
NRXN1-DT	ENST00000779112.1 link	n.165-24677A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0486

AC:

7396

AN:

152116

Hom.:

361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0239

Gnomad AMI

AF:

0.0811

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0671

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0250

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0273

Gnomad OTH

AF:

0.0654

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

GnomAD4 genome

AF:

0.0487

AC:

7409

AN:

152234

Hom.:

365

Cov.:

AF XY:

0.0528

AC XY:

3934

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0240

AC:

996

AN:

41558

American (AMR)

AF:

0.146

AC:

2227

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0671

AC:

233

AN:

3472

East Asian (EAS)

AF:

0.181

AC:

931

AN:

5148

South Asian (SAS)

AF:

0.137

AC:

664

AN:

4830

European-Finnish (FIN)

AF:

0.0250

AC:

265

AN:

10620

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0274

AC:

1860

AN:

68002

Other (OTH)

AF:

0.0671

AC:

142

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

340

680

1020

1360

1700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0369

Hom.:

Bravo

AF:

0.0581

Asia WGS

AF:

0.157

AC:

544

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.30

(source)

DANN

Benign

0.34

PhyloP100

-0.57

Splicing

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

Publications

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ENST00000440698.1:n.616-24677A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over