rs724940

Positions:

• chr20-7218766-A-G

Variant summary

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

The ENST00000449581.1(LINC01428):​n.164+23063T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,888 control chromosomes in the GnomAD database, including 8,350 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 0.29 (8350 hom., cov: 31)
• Consequence: LINC01428 ENST00000449581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

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

ENSG00000238102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.164+23063T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.1	n.164+23063T>C		intron_variant		1
ENSG00000238102	ENST00000702434.1	n.176-27028T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43879 AN: 151770 Hom.: 8319 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.289 AC: 43951 AN: 151888 Hom.: 8350 Cov.: 31 AF XY: 0.285 AC XY: 21129 AN XY: 74220

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.279

Alfa AF: 0.203 Hom.: 6628

Bravo AF: 0.296

Asia WGS AF: 0.174 AC: 608 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724940; hg19: chr20-7199413;