rs13207543

chr6-79826165-C-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01621	ENST00000438797.3	n.233+6990G>T		intron_variant, non_coding_transcript_variant		5
LINC01621	ENST00000669965.1	n.232+6990G>T		intron_variant, non_coding_transcript_variant
LINC01621	ENST00000693479.1	n.373+3498G>T		intron_variant, non_coding_transcript_variant

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;