rs7983232

Variant names:

• chr13-22163460-A-G
• rs7983232
• ENST00000611481.1:n.165+55826A>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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

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

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 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

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;