rs6038726

Positions:

• chr20-7155675-C-G
• chr20-7155675-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.299-7476G>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 0.353 in 152,022 control chromosomes in the GnomAD database, including 11,568 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 0.35 (11568 hom., cov: 32)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01428	NR_110609.1	n.299-7476G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01428	ENST00000449581.1	n.299-7476G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53616 AN: 151904 Hom.: 11532 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.353 AC: 53713 AN: 152022 Hom.: 11568 Cov.: 32 AF XY: 0.347 AC XY: 25821 AN XY: 74310

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.318

Alfa AF: 0.154 Hom.: 262

Bravo AF: 0.372

Asia WGS AF: 0.206 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038726; hg19: chr20-7136322;