chr10-103583143-C-T

Variant names:

• chr10-103583143-C-T
• rs902991
• NM_004210.5:c.650-1393C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004210.5(NEURL1):​c.650-1393C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,058 control chromosomes in the GnomAD database, including 45,797 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 0.77 (45797 hom., cov: 31)
• Consequence: NEURL1 NM_004210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 7 publications found

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]

ENSG00000287419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004210.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEURL1	NM_004210.5	MANE Select	c.650-1393C>T		intron	N/A	NP_004201.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEURL1	ENST00000369780.9	TSL:1 MANE Select	c.650-1393C>T		intron	N/A	ENSP00000358795.4
	ENSG00000287419	ENST00000663302.1		n.545G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117198 AN: 151940 Hom.: 45743 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.771 AC: 117310 AN: 152058 Hom.: 45797 Cov.: 31 AF XY: 0.770 AC XY: 57193 AN XY: 74308

African (AFR) AF: 0.880 AC: 36498 AN: 41492

American (AMR) AF: 0.799 AC: 12207 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2689 AN: 3466

East Asian (EAS) AF: 0.795 AC: 4100 AN: 5158

South Asian (SAS) AF: 0.854 AC: 4117 AN: 4822

European-Finnish (FIN) AF: 0.620 AC: 6536 AN: 10538

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48836 AN: 67980

Other (OTH) AF: 0.782 AC: 1650 AN: 2110

Alfa AF: 0.742 Hom.: 159962

Bravo AF: 0.788

Asia WGS AF: 0.845 AC: 2939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.0
DANN	Benign	0.57
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs902991; hg19: chr10-105342900;