ENST00000791984.1:n.70C>G

Variant names:

• chr6-30516259-G-C
• rs10484552
• ENST00000791984.1:n.70C>G

Variant summary

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

The ENST00000791984.1(ENSG00000303124):​n.70C>G 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 0.0539 in 152,106 control chromosomes in the GnomAD database, including 269 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 0.054 (269 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000303124 ENST00000791984.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 14 publications found

Genes affected

ENSG00000303124 (HGNC:):

LINC02569 (HGNC:39760): (long intergenic non-protein coding RNA 2569)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791984.1. 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
	LINC02569	NR_149088.1		n.-7G>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303124	ENST00000791984.1		n.70C>G		non_coding_transcript_exon	Exon 1 of 2
	LINC02569	ENST00000415195.2	TSL:2	n.-7G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8207 AN: 151988 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0632

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0539 AC: 8202 AN: 152106 Hom.: 269 Cov.: 32 AF XY: 0.0538 AC XY: 4004 AN XY: 74368

African (AFR) AF: 0.0386 AC: 1602 AN: 41492

American (AMR) AF: 0.0403 AC: 615 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 343 AN: 3468

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5172

South Asian (SAS) AF: 0.110 AC: 529 AN: 4818

European-Finnish (FIN) AF: 0.0308 AC: 326 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4457 AN: 67990

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0558 Hom.: 42

Bravo AF: 0.0525

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10484552; hg19: chr6-30484036;