rs16893526

Variant names:

• chr6-81805598-G-A
• rs16893526
• ENST00000848188.1:n.85-12573C>T

Variant summary

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

The ENST00000848188.1(LINC01526):​n.85-12573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 151,894 control chromosomes in the GnomAD database, including 582 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 0.082 (582 hom., cov: 32)
• Consequence: LINC01526 ENST00000848188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 20 publications found

Genes affected

LINC01526 (HGNC:51265): (long intergenic non-protein coding RNA 1526)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01526	ENST00000848188.1	n.85-12573C>T		intron_variant	Intron 1 of 1
LINC01526	ENST00000848189.1	n.193+8431C>T		intron_variant	Intron 2 of 2
LINC01526	ENST00000848190.1	n.667+8431C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12508 AN: 151776 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0824 AC: 12513 AN: 151894 Hom.: 582 Cov.: 32 AF XY: 0.0802 AC XY: 5953 AN XY: 74252

African (AFR) AF: 0.0866 AC: 3591 AN: 41446

American (AMR) AF: 0.0668 AC: 1018 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3466

East Asian (EAS) AF: 0.153 AC: 784 AN: 5112

South Asian (SAS) AF: 0.0992 AC: 478 AN: 4818

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0830 AC: 5636 AN: 67910

Other (OTH) AF: 0.0973 AC: 205 AN: 2106

Alfa AF: 0.0866 Hom.: 2307

Bravo AF: 0.0864

Asia WGS AF: 0.115 AC: 399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs16893526; hg19: chr6-82515315;