rs7071247

Variant names:

• chr10-103498029-G-T
• rs7071247
• NM_004210.5:c.85+3557G>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.85+3557G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,008 control chromosomes in the GnomAD database, including 3,020 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 0.19 (3020 hom., cov: 32)
• Consequence: NEURL1 NM_004210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 17 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]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEURL1	NM_004210.5	MANE Select	c.85+3557G>T		intron	N/A	NP_004201.3
	NEURL1-AS1	NR_120675.1		n.120-3294C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEURL1	ENST00000369780.9	TSL:1 MANE Select	c.85+3557G>T		intron	N/A	ENSP00000358795.4
	NEURL1	ENST00000945279.1		c.85+3557G>T		intron	N/A	ENSP00000615338.1
	NEURL1-AS1	ENST00000453753.5	TSL:5	n.71-3294C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28513 AN: 151890 Hom.: 3011 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0661

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.188 AC: 28550 AN: 152008 Hom.: 3020 Cov.: 32 AF XY: 0.193 AC XY: 14364 AN XY: 74316

African (AFR) AF: 0.234 AC: 9698 AN: 41442

American (AMR) AF: 0.214 AC: 3273 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4816

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9224 AN: 67960

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.163 Hom.: 7293

Bravo AF: 0.190

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		0.076
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: rs7071247; hg19: chr10-105257786;