20-12880455-A-C

Position:

• chr20-12880455-A-C

Variant summary

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

The NR_109868.1(LINC01722):​n.2455+12186T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,124 control chromosomes in the GnomAD database, including 1,192 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 0.12 (1192 hom., cov: 32)
• Consequence: LINC01722 NR_109868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

LINC01722 (HGNC:52510): (long intergenic non-protein coding RNA 1722)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01722	NR_109868.1	n.2455+12186T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01722	ENST00000456265.1	n.2455+12186T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17597 AN: 152006 Hom.: 1190 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.116 AC: 17599 AN: 152124 Hom.: 1192 Cov.: 32 AF XY: 0.113 AC XY: 8380 AN XY: 74378

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0926

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0997 Hom.: 399

Bravo AF: 0.123

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6109595; hg19: chr20-12861103;