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 ENST00000422666.1(LINC01524):​n.93-2142G>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 ENST00000422666.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372666	XR_007067652.1	n.2021+215G>A		intron_variant	Intron 15 of 16
LOC105372666	XR_007067653.1	n.1347+215G>A		intron_variant	Intron 10 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000421642.5	n.400-2142G>A		intron_variant	Intron 4 of 4	5
LINC01524	ENST00000422666.1	n.93-2142G>A		intron_variant	Intron 1 of 2	3
LINC01524	ENST00000425279.6	n.541-2142G>A		intron_variant	Intron 4 of 5	3

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 v4.3

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;