rs11782819

chr8-10477271-T-Cchr8-10477271-T-G

Variant summary

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

The NR_120604.1(LINC03022):n.216T>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 0.536 in 152,118 control chromosomes in the GnomAD database, including 22,025 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 0.54 (22024 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LINC03022 NR_120604.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

Genes affected

LINC03022 (HGNC:56151): (long intergenic non-protein coding RNA 3022)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03022	NR_120604.1	n.216T>C		non_coding_transcript_exon_variant	2/5
LOC124901887	XR_007060821.1	n.746A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03022	ENST00000524047.5	n.216T>C		non_coding_transcript_exon_variant	2/5	4
	ENST00000671169.1	n.780A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81452 AN: 151992 Hom.: 22009 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.580

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.536 AC: 81506 AN: 152110 Hom.: 22024 Cov.: 32 AF XY: 0.537 AC XY: 39929 AN XY: 74364

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.576

Alfa AF: 0.523 Hom.: 43627

Bravo AF: 0.527

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.18
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11782819; hg19: chr8-10334781;