Genetic Variant NEURL1:c.85+236T>C (chr10-103494708-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004210.5(NEURL1):c.85+236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NEURL1
NM_004210.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.545

Publications

0 publications found

Variant links:

Genes affected

NEURL1 (HGNC:7761): (neuralized E3 ubiquitin protein ligase 1) Predicted to enable translation factor activity, non-nucleic acid binding and ubiquitin protein ligase activity. Involved in negative regulation of Notch signaling pathway; negative regulation of cell population proliferation; and positive regulation of apoptotic process. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

NEURL1 links:

NEURL1-AS1 (HGNC:51220): (NEURL1 antisense RNA 1)

NEURL1-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEURL1	NM_004210.5 link	c.85+236T>C		intron_variant	Intron 1 of 5	ENST00000369780.9	NP_004201.3
NEURL1-AS1	NR_120675.1 link	n.147A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NEURL1	ENST00000369780.9 link	c.85+236T>C	intron_variant	Intron 1 of 5	1	NM_004210.5	ENSP00000358795.4	O76050-1
NEURL1-AS1	ENST00000453753.5 link	n.98A>G	non_coding_transcript_exon_variant	Exon 3 of 4	5
NEURL1-AS1	ENST00000783100.1 link	n.104-14711A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

374694

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

197468

African (AFR)

AF:

0.00

AC:

AN:

7804

American (AMR)

AF:

0.00

AC:

AN:

11366

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11732

East Asian (EAS)

AF:

0.00

AC:

AN:

23242

South Asian (SAS)

AF:

0.00

AC:

AN:

36762

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27572

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1750

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

232040

Other (OTH)

AF:

0.00

AC:

AN:

22426

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.55

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over