ENST00000452494.3:n.1536G>A

Variant names:

• chr10-99528007-G-A
• rs10883365
• ENST00000452494.3:n.1536G>A

Variant summary

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

The ENST00000452494.3(ENSG00000228778):​n.1536G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,748 control chromosomes in the GnomAD database, including 20,944 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 0.52 (20885 hom., cov: 34)
  • Exomes 𝑓: 0.43 (59 hom.)
• Consequence: ENSG00000228778 ENST00000452494.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 84 publications found

Genes affected

ENSG00000228778 (HGNC:):

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01475	NR_120618.1	n.376C>T		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228778	ENST00000452494.3	n.1536G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC01475	ENST00000548010.2	n.453C>T		non_coding_transcript_exon_variant	Exon 3 of 6	1
LINC01475	ENST00000795233.1	n.408C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79428 AN: 151930 Hom.: 20863 Cov.: 34

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.431 AC: 302 AN: 700 Hom.: 59 Cov.: 0 AF XY: 0.425 AC XY: 169 AN XY: 398

African (AFR) AF: 0.607 AC: 17 AN: 28

American (AMR) AF: 0.400 AC: 4 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 8 AN: 18

East Asian (EAS) AF: 0.486 AC: 34 AN: 70

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.410 AC: 32 AN: 78

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.412 AC: 182 AN: 442

Other (OTH) AF: 0.480 AC: 24 AN: 50

GnomAD4 genome AF: 0.523 AC: 79491 AN: 152048 Hom.: 20885 Cov.: 34 AF XY: 0.525 AC XY: 38997 AN XY: 74330

African (AFR) AF: 0.513 AC: 21268 AN: 41432

American (AMR) AF: 0.565 AC: 8640 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2857 AN: 5174

South Asian (SAS) AF: 0.627 AC: 3028 AN: 4832

European-Finnish (FIN) AF: 0.510 AC: 5400 AN: 10586

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35061 AN: 67944

Other (OTH) AF: 0.500 AC: 1055 AN: 2108

Alfa AF: 0.518 Hom.: 89296

Bravo AF: 0.524

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10883365; hg19: chr10-101287764;