ENST00000505156.2:n.1559-32663C>A

Variant names:

• chr8-116010099-G-T
• rs2223065
• ENST00000505156.2:n.1559-32663C>A

Variant summary

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

The ENST00000505156.2(LINC00536):​n.1559-32663C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,022 control chromosomes in the GnomAD database, including 304 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 0.040 (304 hom., cov: 32)
• Consequence: LINC00536 ENST00000505156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 2 publications found

Genes affected

LINC00536 (HGNC:43645): (long intergenic non-protein coding RNA 536)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505156.2. 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
	LINC00536	NR_046215.1		n.1559-32663C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00536	ENST00000505156.2	TSL:1	n.1559-32663C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6043 AN: 151904 Hom.: 300 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.00953

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0398 AC: 6050 AN: 152022 Hom.: 304 Cov.: 32 AF XY: 0.0444 AC XY: 3302 AN XY: 74318

African (AFR) AF: 0.0229 AC: 952 AN: 41516

American (AMR) AF: 0.129 AC: 1960 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5170

South Asian (SAS) AF: 0.133 AC: 639 AN: 4822

European-Finnish (FIN) AF: 0.00953 AC: 101 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1273 AN: 67884

Other (OTH) AF: 0.0413 AC: 87 AN: 2108

Alfa AF: 0.0264 Hom.: 278

Bravo AF: 0.0435

Asia WGS AF: 0.133 AC: 459 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	12
DANN	Benign	0.46
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2223065; hg19: chr8-117022324;