rs6651252

Variant names:

• chr8-128554935-T-C
• rs6651252
• ENST00000756966.1:n.99T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000756966.1(ENSG00000298619):​n.99T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,100 control chromosomes in the GnomAD database, including 3,232 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 0.18 (3232 hom., cov: 32)
• Consequence: ENSG00000298619 ENST00000756966.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 78 publications found

Genes affected

ENSG00000298619 (HGNC:):

LINC00824 (HGNC:50281): (long intergenic non-protein coding RNA 824)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756966.1. 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
	LINC00824	NR_121672.1		n.508+6135A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298619	ENST00000756966.1		n.99T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298619	ENST00000756967.1		n.153T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298619	ENST00000756968.1		n.151T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27462 AN: 151982 Hom.: 3230 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.181 AC: 27490 AN: 152100 Hom.: 3232 Cov.: 32 AF XY: 0.176 AC XY: 13122 AN XY: 74372

African (AFR) AF: 0.336 AC: 13929 AN: 41444

American (AMR) AF: 0.111 AC: 1695 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3466

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5172

South Asian (SAS) AF: 0.116 AC: 560 AN: 4818

European-Finnish (FIN) AF: 0.125 AC: 1325 AN: 10600

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8969 AN: 68000

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.144 Hom.: 8957

Bravo AF: 0.187

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.45
PhyloP100		0.087

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: rs6651252;

hg19: chr8-129567181;