6-137755016-T-C

Variant names:

• chr6-137755016-T-C
• rs6927210
• ENST00000635999.1:n.434-8801T>C

Variant summary

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

The ENST00000645996.1(LINC02539):​n.214-24419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,050 control chromosomes in the GnomAD database, including 24,838 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 0.56 (24838 hom., cov: 32)
• Consequence: LINC02539 ENST00000645996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 14 publications found

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

LINC02539 (HGNC:53572): (long intergenic non-protein coding RNA 2539)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645996.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.434-8801T>C		intron	N/A
	LINC02539	ENST00000645996.1		n.214-24419A>G		intron	N/A
	LINC02539	ENST00000821781.1		n.279-24419A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85354 AN: 151932 Hom.: 24803 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.562 AC: 85444 AN: 152050 Hom.: 24838 Cov.: 32 AF XY: 0.563 AC XY: 41816 AN XY: 74320

African (AFR) AF: 0.678 AC: 28094 AN: 41434

American (AMR) AF: 0.507 AC: 7751 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4248 AN: 5182

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4824

European-Finnish (FIN) AF: 0.519 AC: 5491 AN: 10574

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34473 AN: 67972

Other (OTH) AF: 0.553 AC: 1168 AN: 2114

Alfa AF: 0.515 Hom.: 34788

Bravo AF: 0.567

Asia WGS AF: 0.662 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.54

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: rs6927210;

hg19: chr6-138076153;