13-22163460-A-G

Position:

• chr13-22163460-A-G

Variant summary

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

The ENST00000631321.1(LINC00540):​n.411-111063A>G 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 0.351 in 151,660 control chromosomes in the GnomAD database, including 9,487 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 0.35 (9487 hom., cov: 32)
• Consequence: LINC00540 ENST00000631321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

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 (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00540	ENST00000631321.1	n.411-111063A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53153 AN: 151540 Hom.: 9474 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.317

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.351 AC: 53216 AN: 151660 Hom.: 9487 Cov.: 32 AF XY: 0.352 AC XY: 26103 AN XY: 74084

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.359

Alfa AF: 0.321 Hom.: 8283

Bravo AF: 0.358

Asia WGS AF: 0.410 AC: 1415 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7983232; hg19: chr13-22737599;