20-20972669-G-C

Variant names:

• chr20-20972669-G-C
• rs733578
• ENST00000432942.2:n.*103G>C

Variant summary

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

The ENST00000432942.2(LINC03083):​n.*103G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,282 control chromosomes in the GnomAD database, including 1,084 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 0.061 (1083 hom., cov: 32)
  • Exomes 𝑓: 0.048 (1 hom.)
• Consequence: LINC03083 ENST00000432942.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 1 publications found

Genes affected

LINC03083 (HGNC:56677): (long intergenic non-protein coding RNA 3083)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03083	NR_186504.1	n.*107G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03083	ENST00000432942.2	n.*103G>C		downstream_gene_variant		3
LINC03083	ENST00000750958.1	n.*105G>C		downstream_gene_variant
LINC03083	ENST00000750959.1	n.*105G>C		downstream_gene_variant
LINC03083	ENST00000750960.1	n.*105G>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9256 AN: 152038 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0636

GnomAD4 exome AF: 0.0476 AC: 6 AN: 126 Hom.: 1 AF XY: 0.0543 AC XY: 5 AN XY: 92

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0192 AC: 2 AN: 104

Other (OTH) AF: 0.00 AC: 0 AN: 4

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000114836), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0609 AC: 9264 AN: 152156 Hom.: 1083 Cov.: 32 AF XY: 0.0685 AC XY: 5095 AN XY: 74380

African (AFR) AF: 0.0102 AC: 424 AN: 41518

American (AMR) AF: 0.147 AC: 2250 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2728 AN: 5156

South Asian (SAS) AF: 0.150 AC: 721 AN: 4822

European-Finnish (FIN) AF: 0.0746 AC: 789 AN: 10582

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1977 AN: 68000

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0187 Hom.: 16

Bravo AF: 0.0666

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.71
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs733578; hg19: chr20-20953310;