rs6117692

Variant names:

• chr20-7207064-G-A
• rs6117692
• ENST00000449581.2:n.165-18497C>T

Variant summary

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

The ENST00000449581.2(LINC01428):​n.165-18497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,964 control chromosomes in the GnomAD database, including 2,946 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 0.17 (2946 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

LINC01428 (HGNC:50738): (long intergenic non-protein coding RNA 1428)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449581.2. 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
	LINC01428	NR_110609.1		n.165-18497C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	ENST00000449581.2	TSL:1	n.165-18497C>T		intron	N/A
	LINC01428	ENST00000702434.1		n.176-15326C>T		intron	N/A
	LINC01428	ENST00000716639.1		n.173+51034C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26488 AN: 151846 Hom.: 2945 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.174 AC: 26491 AN: 151964 Hom.: 2946 Cov.: 32 AF XY: 0.173 AC XY: 12826 AN XY: 74260

African (AFR) AF: 0.0440 AC: 1825 AN: 41452

American (AMR) AF: 0.264 AC: 4031 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.136 AC: 706 AN: 5176

South Asian (SAS) AF: 0.0739 AC: 355 AN: 4804

European-Finnish (FIN) AF: 0.232 AC: 2439 AN: 10522

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16162 AN: 67962

Other (OTH) AF: 0.173 AC: 365 AN: 2106

Alfa AF: 0.205 Hom.: 456

Bravo AF: 0.173

Asia WGS AF: 0.0930 AC: 323 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.30
PhyloP100		-1.2

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: rs6117692;

hg19: chr20-7187711;