rs2503340

Positions:

• chr13-22236825-C-A

Variant summary

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

The NR_103810.1(LINC00540):​n.144+26397C>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 0.771 in 152,130 control chromosomes in the GnomAD database, including 45,649 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 0.77 (45649 hom., cov: 32)
• Consequence: LINC00540 NR_103810.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

LINC00540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00540	NR_103810.1	n.144+26397C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.411-37698C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117199 AN: 152012 Hom.: 45630 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.771 AC: 117268 AN: 152130 Hom.: 45649 Cov.: 32 AF XY: 0.771 AC XY: 57355 AN XY: 74368

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.766

Alfa AF: 0.810 Hom.: 88278

Bravo AF: 0.759

Asia WGS AF: 0.784 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2503340; hg19: chr13-22810964;