rs13207543

Variant names:

• chr6-79826165-C-A
• rs13207543
• ENST00000438797.3:n.233+6990G>T

Variant summary

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

The ENST00000438797.3(LINC01621):​n.233+6990G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,156 control chromosomes in the GnomAD database, including 1,322 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 0.12 (1322 hom., cov: 33)
• Consequence: LINC01621 ENST00000438797.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

LINC01621 (HGNC:14109): (long intergenic non-protein coding RNA 1621)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 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
LINC01621	ENST00000438797.3	n.233+6990G>T		intron_variant	Intron 1 of 3	5
LINC01621	ENST00000669965.1	n.232+6990G>T		intron_variant	Intron 1 of 3
LINC01621	ENST00000693479.1	n.373+3498G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17956 AN: 152038 Hom.: 1322 Cov.: 33

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0706

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.118 AC: 17950 AN: 152156 Hom.: 1322 Cov.: 33 AF XY: 0.120 AC XY: 8900 AN XY: 74378

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.137

Alfa AF: 0.152 Hom.: 1547

Bravo AF: 0.113

Asia WGS AF: 0.108 AC: 376 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13207543; hg19: chr6-80535882;