rs856337

Variant names:

• chr20-52688380-G-A
• rs856337
• ENST00000421642.5:n.400-2142G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-52688380-G-A
• chr20-52688380-G-C
• chr20-52688380-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421642.5(LINC01524):​n.400-2142G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 152,280 control chromosomes in the GnomAD database, including 73,782 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 0.98 (73782 hom., cov: 31)
• Consequence: LINC01524 ENST00000421642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 0 publications found

Genes affected

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

LOC105372666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421642.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01524	ENST00000421642.5	TSL:5	n.400-2142G>A		intron	N/A
	LINC01524	ENST00000422666.1	TSL:3	n.93-2142G>A		intron	N/A
	LINC01524	ENST00000425279.6	TSL:3	n.541-2142G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149756 AN: 152162 Hom.: 73728 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.984 AC: 149867 AN: 152280 Hom.: 73782 Cov.: 31 AF XY: 0.981 AC XY: 73047 AN XY: 74454

African (AFR) AF: 0.996 AC: 41396 AN: 41554

American (AMR) AF: 0.975 AC: 14925 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3462 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4990 AN: 5172

South Asian (SAS) AF: 0.961 AC: 4632 AN: 4818

European-Finnish (FIN) AF: 0.944 AC: 10018 AN: 10610

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67156 AN: 68034

Other (OTH) AF: 0.987 AC: 2085 AN: 2112

Alfa AF: 0.987 Hom.: 9196

Bravo AF: 0.987

Asia WGS AF: 0.960 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs856337; hg19: chr20-51304919;