rs698739

Variant names:

• chr8-116218780-C-A
• rs698739
• ENST00000505156.2:n.1333+40712G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-116218780-C-A
• chr8-116218780-C-G
• chr8-116218780-C-T

Variant summary

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

The ENST00000505156.2(LINC00536):​n.1333+40712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,156 control chromosomes in the GnomAD database, including 5,854 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 0.23 (5854 hom., cov: 32)
• Consequence: LINC00536 ENST00000505156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00536	NR_046215.1		n.1333+40712G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00536	ENST00000505156.2	TSL:1	n.1333+40712G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35594 AN: 152038 Hom.: 5828 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.234 AC: 35659 AN: 152156 Hom.: 5854 Cov.: 32 AF XY: 0.232 AC XY: 17264 AN XY: 74420

African (AFR) AF: 0.473 AC: 19624 AN: 41482

American (AMR) AF: 0.154 AC: 2355 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3468

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5168

South Asian (SAS) AF: 0.187 AC: 903 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1332 AN: 10604

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 10027 AN: 68006

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.191 Hom.: 523

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs698739;

hg19: chr8-117231025;