chr13-22163460-A-G

Variant names:

• chr13-22163460-A-G
• rs7983232
• ENST00000611481.1:n.165+55826A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611481.1(LINC00540):​n.165+55826A>G variant causes a intron 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 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 4 publications found

Genes affected

LINC00540 (HGNC:43673): (long intergenic non-protein coding RNA 540)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000611481.1	n.165+55826A>G		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-111063A>G		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.414-20473A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.414 AC: 17155 AN: 41392

American (AMR) AF: 0.363 AC: 5534 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1272 AN: 3458

East Asian (EAS) AF: 0.413 AC: 2128 AN: 5150

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3081 AN: 10480

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20972 AN: 67816

Other (OTH) AF: 0.359 AC: 755 AN: 2104

Alfa AF: 0.327 Hom.: 22845

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7983232; hg19: chr13-22737599;