rs6085938

chr20-7240283-A-Gchr20-7240283-A-T

Variant summary

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

The NR_110609.1(LINC01428):n.164+1546T>C 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 0.398 in 152,022 control chromosomes in the GnomAD database, including 13,835 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 (13835 hom., cov: 31)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.164+1546T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.164+1546T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000702434.1	n.175+17815T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60536 AN: 151902 Hom.: 13843 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.398 AC: 60542 AN: 152022 Hom.: 13835 Cov.: 31 AF XY: 0.405 AC XY: 30125 AN XY: 74296

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.414

Alfa AF: 0.469 Hom.: 8217

Bravo AF: 0.385

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085938; hg19: chr20-7220930;