rs4811340

Positions:

• chr20-52393218-G-C

Variant summary

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

The ENST00000666751.1(LINC01524):​n.173+37859G>C 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 0.444 in 151,982 control chromosomes in the GnomAD database, including 16,668 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 0.44 (16668 hom., cov: 32)
• Consequence: LINC01524 ENST00000666751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.462+52566G>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.425+52566G>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754671.2	n.425+52566G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01524	ENST00000666751.1	n.173+37859G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67413 AN: 151864 Hom.: 16615 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.444 AC: 67532 AN: 151982 Hom.: 16668 Cov.: 32 AF XY: 0.437 AC XY: 32427 AN XY: 74272

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.429

Alfa AF: 0.403 Hom.: 1669

Bravo AF: 0.461

Asia WGS AF: 0.415 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.38
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811340; hg19: chr20-51009757;