20-7214742-G-T

Variant summary

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

The NR_110609.1(LINC01428):n.165-26175C>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 0.203 in 152,018 control chromosomes in the GnomAD database, including 5,658 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 0.20 (5658 hom., cov: 31)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.165-26175C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.165-26175C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000702434.1	n.176-23004C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30858 AN: 151900 Hom.: 5626 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.203 AC: 30932 AN: 152018 Hom.: 5658 Cov.: 31 AF XY: 0.201 AC XY: 14908 AN XY: 74324

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.205

Alfa AF: 0.119 Hom.: 425

Bravo AF: 0.216

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.57
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038742; hg19: chr20-7195389;