8-116237363-G-C

Position:

• chr8-116237363-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046215.1(LINC00536):​n.1333+22129C>G variant causes a intron, non coding transcript 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 NR_046215.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00536	NR_046215.1	n.1333+22129C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00536	ENST00000505156.2	n.1333+22129C>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.718

Alfa AF: 0.656 Hom.: 2102

Bravo AF: 0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs799890; hg19: chr8-117249601;