16-52078460-T-G

Variant summary

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

The ENST00000568524.5(LINC02911):n.15A>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 0.145 in 152,192 control chromosomes in the GnomAD database, including 1,905 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 0.15 (1905 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02911 ENST00000568524.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

LINC02911 (HGNC:44658): (long intergenic non-protein coding RNA 2911)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02911	XR_004837540.2	n.58A>C		non_coding_transcript_exon_variant	1/8
LINC02911	XR_007065208.1	n.58A>C		non_coding_transcript_exon_variant	1/8
LINC02911	XR_007065209.1	n.58A>C		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02911	ENST00000568524.5	n.15A>C		non_coding_transcript_exon_variant	1/4	5

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22119 AN: 152074 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.159

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.145 AC: 22123 AN: 152192 Hom.: 1905 Cov.: 32 AF XY: 0.143 AC XY: 10603 AN XY: 74394

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.155

Alfa AF: 0.175 Hom.: 4762

Bravo AF: 0.148

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.8
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3743795; hg19: chr16-52112372;