rs6117692

chr20-7207064-G-A

Variant summary

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

The NR_110609.1(LINC01428):n.165-18497C>T 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 0.174 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 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.165-18497C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.165-18497C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000702434.1	n.176-15326C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0440

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0739

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.173

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.32
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6117692; hg19: chr20-7187711;