rs6140226

chr20-7245836-C-T

Variant summary

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

The NR_110609.1(LINC01428):n.117-3960G>A 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 0.396 in 152,080 control chromosomes in the GnomAD database, including 13,452 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 0.40 (13452 hom., cov: 32)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.117-3960G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.117-3960G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000702434.1	n.175+12262G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60259 AN: 151960 Hom.: 13461 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.396 AC: 60269 AN: 152080 Hom.: 13452 Cov.: 32 AF XY: 0.404 AC XY: 30005 AN XY: 74344

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.411

Alfa AF: 0.453 Hom.: 16949

Bravo AF: 0.383

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6140226; hg19: chr20-7226483;