rs12853883

chr13-22057036-G-A

Variant summary

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

The ENST00000631321.1(LINC00540):n.410+15652G>A 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 0.036 in 151,082 control chromosomes in the GnomAD database, including 132 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 0.036 (132 hom., cov: 31)
• Consequence: LINC00540 ENST00000631321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

LINC00540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370108	XR_007063716.1	n.415-6937G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00540	ENST00000631321.1	n.410+15652G>A		intron_variant, non_coding_transcript_variant		2
LINC00540	ENST00000657205.1	n.413+15652G>A		intron_variant, non_coding_transcript_variant
LINC00540	ENST00000690279.1	n.410+15652G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5438 AN: 151044 Hom.: 133 Cov.: 31

Gnomad AFR AF: 0.00859

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0329

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

GnomAD4 genome AF: 0.0360 AC: 5435 AN: 151082 Hom.: 132 Cov.: 31 AF XY: 0.0368 AC XY: 2710 AN XY: 73622

Gnomad4 AFR AF: 0.00858

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.0285

Gnomad4 FIN AF: 0.0691

Gnomad4 NFE AF: 0.0457

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0420 Hom.: 194

Bravo AF: 0.0331

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.093
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12853883; hg19: chr13-22631175;