5-135236539-A-T

Variant summary

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

The NR_037895.1(LINC02900):n.1855T>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 0.0394 in 151,944 control chromosomes in the GnomAD database, including 230 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 0.039 (230 hom., cov: 29)
  • Exomes 𝑓: 0.013 (0 hom.)
• Consequence: LINC02900 NR_037895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

LINC02900 (HGNC:27964): (long intergenic non-protein coding RNA 2900)

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02900	NR_037895.1	n.1855T>A		non_coding_transcript_exon_variant	4/4
PITX1-AS1	NR_161235.1	n.467+62367A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02900	ENST00000505663.1	n.1857T>A		non_coding_transcript_exon_variant	4/4	1
PITX1-AS1	ENST00000624272.3	n.461+62367A>T		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000513931.2	n.341-59956A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5948 AN: 151588 Hom.: 225 Cov.: 29

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00518

Gnomad OTH AF: 0.0383

GnomAD4 exome AF: 0.0126 AC: 3 AN: 238 Hom.: 0 Cov.: 0 AF XY: 0.00735 AC XY: 1 AN XY: 136

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0259

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0394 AC: 5980 AN: 151706 Hom.: 230 Cov.: 29 AF XY: 0.0418 AC XY: 3101 AN XY: 74108

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.0745

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.00518

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.000873 Hom.: 13675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs606854; hg19: chr5-134572229;