chr8-90558134-A-G

Variant names:

• chr8-90558134-A-G
• rs1018836
• ENST00000521975.2:n.247-3468T>C

Variant summary

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

The ENST00000524361.5(LINC00534):​n.437-11001A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,062 control chromosomes in the GnomAD database, including 17,588 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 0.47 (17588 hom., cov: 32)
• Consequence: LINC00534 ENST00000524361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 8 publications found

Genes affected

LINC01030 (HGNC:49016): (long intergenic non-protein coding RNA 1030)

LINC00534 (HGNC:43643): (long intergenic non-protein coding RNA 534)

LOC124901975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524361.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01030	ENST00000521975.2	TSL:5	n.247-3468T>C		intron	N/A
	LINC00534	ENST00000524361.5	TSL:3	n.437-11001A>G		intron	N/A
	LINC00534	ENST00000653734.1		n.443-24370A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70774 AN: 151944 Hom.: 17544 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.466 AC: 70879 AN: 152062 Hom.: 17588 Cov.: 32 AF XY: 0.468 AC XY: 34759 AN XY: 74342

African (AFR) AF: 0.597 AC: 24767 AN: 41470

American (AMR) AF: 0.581 AC: 8869 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3466

East Asian (EAS) AF: 0.717 AC: 3701 AN: 5160

South Asian (SAS) AF: 0.357 AC: 1721 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3711 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25342 AN: 67966

Other (OTH) AF: 0.464 AC: 979 AN: 2112

Alfa AF: 0.409 Hom.: 9183

Bravo AF: 0.493

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.42
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1018836; hg19: chr8-91570362;