8-116237363-G-C

Variant names:

• chr8-116237363-G-C
• rs799890
• ENST00000505156.2:n.1333+22129C>G

Variant summary

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

The ENST00000505156.2(LINC00536):​n.1333+22129C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,036 control chromosomes in the GnomAD database, including 36,890 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 0.68 (36890 hom., cov: 31)
• Consequence: LINC00536 ENST00000505156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 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.1333+22129C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00536	ENST00000505156.2	TSL:1	n.1333+22129C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103602 AN: 151916 Hom.: 36865 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.682 AC: 103663 AN: 152036 Hom.: 36890 Cov.: 31 AF XY: 0.675 AC XY: 50159 AN XY: 74300

African (AFR) AF: 0.515 AC: 21355 AN: 41448

American (AMR) AF: 0.570 AC: 8698 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2810 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2612 AN: 5164

South Asian (SAS) AF: 0.559 AC: 2690 AN: 4810

European-Finnish (FIN) AF: 0.748 AC: 7901 AN: 10562

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55103 AN: 67994

Other (OTH) AF: 0.718 AC: 1516 AN: 2110

Alfa AF: 0.656 Hom.: 2102

Bravo AF: 0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs799890; hg19: chr8-117249601;