rs6038729

Variant names:

• chr20-7157110-A-C
• rs6038729
• ENST00000449581.2:n.299-8911T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-7157110-A-C
• chr20-7157110-A-T

Variant summary

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

The ENST00000449581.2(LINC01428):​n.299-8911T>G variant causes a intron 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 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449581.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	NR_110609.1		n.299-8911T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	ENST00000449581.2	TSL:1	n.299-8911T>G		intron	N/A
	LINC01428	ENST00000716639.1		n.174-8911T>G		intron	N/A

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

African (AFR) AF: 0.673 AC: 27856 AN: 41414

American (AMR) AF: 0.396 AC: 6046 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1127 AN: 5154

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10558

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21427 AN: 67952

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.349 Hom.: 31467

Bravo AF: 0.432

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.079
DANN	Benign	0.37
PhyloP100		-0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6038729;

hg19: chr20-7137757;