rs3014185

Positions:

• chr10-103488977-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120675.1(NEURL1-AS1):​n.294+5584G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEURL1-AS1	NR_120675.1	n.294+5584G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEURL1-AS1	ENST00000453753.5	n.245+5584G>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.786

Alfa AF: 0.783 Hom.: 5801

Bravo AF: 0.801

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3014185; hg19: chr10-105248734;