rs6022029

chr20-52658626-A-G

Variant summary

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

The ENST00000666751.1(LINC01524):n.642-8093A>G 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 0.0905 in 152,146 control chromosomes in the GnomAD database, including 1,211 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 0.090 (1211 hom., cov: 32)
• Consequence: LINC01524 ENST00000666751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

LINC01524 (HGNC:51228): (long intergenic non-protein coding RNA 1524)

LOC105372666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.931-10522A>G		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.894-10522A>G		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.257-10522A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01524	ENST00000666751.1	n.642-8093A>G		intron_variant, non_coding_transcript_variant
LINC01524	ENST00000656362.1	n.722-10522A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13693 AN: 152028 Hom.: 1191 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0905 AC: 13764 AN: 152146 Hom.: 1211 Cov.: 32 AF XY: 0.0896 AC XY: 6665 AN XY: 74382

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0188

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0440 Hom.: 177

Bravo AF: 0.103

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6022029; hg19: chr20-51275165;