rs1555823

Variant names:

• chr10-103479506-T-A
• rs1555823
• ENST00000453753.5:n.*97A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-103479506-T-A
• chr10-103479506-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000453753.5(NEURL1-AS1):​n.*97A>T variant causes a downstream gene 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-AS1 ENST00000453753.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 7 publications found

Genes affected

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

ACMG classification

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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEURL1-AS1	NR_120675.1	n.*97A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEURL1-AS1	ENST00000453753.5	n.*97A>T		downstream_gene_variant		5
NEURL1-AS1	ENST00000783100.1	n.*97A>T		downstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 5164 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2674

African (AFR) AF: 0.00 AC: 0 AN: 198

American (AMR) AF: 0.00 AC: 0 AN: 1156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 114

East Asian (EAS) AF: 0.00 AC: 0 AN: 198

South Asian (SAS) AF: 0.00 AC: 0 AN: 326

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 72

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 10

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2830

Other (OTH) AF: 0.00 AC: 0 AN: 260

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-0.57
PromoterAI		0.0096	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1555823; hg19: chr10-105239263;