rs6028335

Variant names:

• chr20-39216834-A-G
• rs6028335
• ENST00000412672.1:n.195-722T>C

Variant summary

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

The ENST00000412672.1(LINC01734):​n.195-722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,120 control chromosomes in the GnomAD database, including 2,438 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 0.16 (2438 hom., cov: 32)
• Consequence: LINC01734 ENST00000412672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 12 publications found

Genes affected

LINC01734 (HGNC:52522): (long intergenic non-protein coding RNA 1734)

ENSG00000300599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412672.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01734	NR_027124.1		n.195-722T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01734	ENST00000412672.1	TSL:1	n.195-722T>C		intron	N/A
	ENSG00000300599	ENST00000772859.1		n.297-2753A>G		intron	N/A
	ENSG00000300599	ENST00000772860.1		n.152-2753A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24824 AN: 152002 Hom.: 2440 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.163 AC: 24825 AN: 152120 Hom.: 2438 Cov.: 32 AF XY: 0.164 AC XY: 12180 AN XY: 74366

African (AFR) AF: 0.0589 AC: 2445 AN: 41544

American (AMR) AF: 0.160 AC: 2444 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3468

East Asian (EAS) AF: 0.0947 AC: 491 AN: 5184

South Asian (SAS) AF: 0.179 AC: 862 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1987 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14765 AN: 67942

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.202 Hom.: 10519

Bravo AF: 0.159

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6028335; hg19: chr20-37845477;