13-22195400-G-A

Position:

• chr13-22195400-G-A

Variant summary

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

The ENST00000631321.1(LINC00540):​n.411-79123G>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 0.232 in 151,924 control chromosomes in the GnomAD database, including 4,607 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 0.23 (4607 hom., cov: 33)
• Consequence: LINC00540 ENST00000631321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

LINC00540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.411-79123G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35266 AN: 151806 Hom.: 4610 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.232 AC: 35280 AN: 151924 Hom.: 4607 Cov.: 33 AF XY: 0.234 AC XY: 17333 AN XY: 74226

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.243

Alfa AF: 0.278 Hom.: 6721

Bravo AF: 0.228

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17326684; hg19: chr13-22769539;