chr10-103488977-C-A

Variant names:

• chr10-103488977-C-A
• rs3014185
• ENST00000453753.5:n.245+5584G>T

Variant summary

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

The NR_120675.1(NEURL1-AS1):​n.294+5584G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,146 control chromosomes in the GnomAD database, including 48,458 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 0.80 (48458 hom., cov: 33)
• Consequence: NEURL1-AS1 NR_120675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 0 publications found

Genes affected

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120675.1. 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-AS1	NR_120675.1		n.294+5584G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEURL1-AS1	ENST00000453753.5	TSL:5	n.245+5584G>T		intron	N/A
	NEURL1-AS1	ENST00000783100.1		n.104-8980G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121016 AN: 152028 Hom.: 48400 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.796 AC: 121133 AN: 152146 Hom.: 48458 Cov.: 33 AF XY: 0.799 AC XY: 59441 AN XY: 74382

African (AFR) AF: 0.820 AC: 34040 AN: 41492

American (AMR) AF: 0.822 AC: 12577 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2741 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5185 AN: 5194

South Asian (SAS) AF: 0.901 AC: 4340 AN: 4816

European-Finnish (FIN) AF: 0.746 AC: 7891 AN: 10572

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51914 AN: 67990

Other (OTH) AF: 0.786 AC: 1662 AN: 2114

Alfa AF: 0.784 Hom.: 6058

Bravo AF: 0.801

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.47
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs3014185; hg19: chr10-105248734;