rs6038729

chr20-7157110-A-Cchr20-7157110-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.299-8911T>G 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 0.413 in 151,944 control chromosomes in the GnomAD database, including 15,105 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 0.41 (15105 hom., cov: 31)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.299-8911T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.299-8911T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62720 AN: 151828 Hom.: 15067 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.413 AC: 62816 AN: 151944 Hom.: 15105 Cov.: 31 AF XY: 0.407 AC XY: 30231 AN XY: 74282

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.404

Alfa AF: 0.326 Hom.: 16433

Bravo AF: 0.432

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.079
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038729; hg19: chr20-7137757;