rs6038727

Variant names:

• chr20-7155710-C-G
• rs6038727
• ENST00000449581.2:n.299-7511G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449581.2(LINC01428):​n.299-7511G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,070 control chromosomes in the GnomAD database, including 7,798 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 0.31 (7798 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.299-7511G>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.299-7511G>C		intron_variant	Intron 5 of 7	1
LINC01428	ENST00000716638.2	n.105+118G>C		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.174-7511G>C		intron_variant	Intron 1 of 2
LINC01428	ENST00000828086.1	n.105+118G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46366 AN: 151952 Hom.: 7777 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.305 AC: 46433 AN: 152070 Hom.: 7798 Cov.: 32 AF XY: 0.301 AC XY: 22357 AN XY: 74348

African (AFR) AF: 0.443 AC: 18389 AN: 41482

American (AMR) AF: 0.325 AC: 4958 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3464

East Asian (EAS) AF: 0.172 AC: 890 AN: 5176

South Asian (SAS) AF: 0.174 AC: 837 AN: 4820

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10572

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17325 AN: 67972

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.287 Hom.: 850

Bravo AF: 0.317

Asia WGS AF: 0.190 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6038727; hg19: chr20-7136357;