rs6109595

Variant names:

• chr20-12880455-A-C
• rs6109595
• ENST00000456265.1:n.2455+12186T>G

Variant summary

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

The ENST00000456265.1(LINC01722):​n.2455+12186T>G variant causes a intron 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 ENST00000456265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456265.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01722	NR_109868.1		n.2455+12186T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01722	ENST00000456265.1	TSL:1	n.2455+12186T>G		intron	N/A

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

African (AFR) AF: 0.185 AC: 7689 AN: 41506

American (AMR) AF: 0.0926 AC: 1414 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3472

East Asian (EAS) AF: 0.0508 AC: 262 AN: 5156

South Asian (SAS) AF: 0.0769 AC: 371 AN: 4822

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10620

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6525 AN: 67966

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.0980 Hom.: 516

Bravo AF: 0.123

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6109595;

hg19: chr20-12861103;