6-137764111-C-T

Variant names:

• chr6-137764111-C-T
• rs7753394
• ENST00000821783.1:n.444G>A

Variant summary

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

The ENST00000821783.1(LINC02539):​n.444G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,194 control chromosomes in the GnomAD database, including 18,625 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 0.49 (18611 hom., cov: 32)
  • Exomes 𝑓: 0.49 (14 hom.)
• Consequence: LINC02539 ENST00000821783.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 16 publications found

Genes affected

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

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02539	ENST00000821783.1	n.444G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02539	ENST00000645996.1	n.213+20621G>A		intron_variant	Intron 2 of 2
LINC02539	ENST00000821781.1	n.278+16029G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74352 AN: 151932 Hom.: 18616 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.484

GnomAD4 exome AF: 0.493 AC: 71 AN: 144 Hom.: 14 AF XY: 0.512 AC XY: 42 AN XY: 82

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.493 AC: 68 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.489 AC: 74372 AN: 152050 Hom.: 18611 Cov.: 32 AF XY: 0.490 AC XY: 36391 AN XY: 74334

African (AFR) AF: 0.454 AC: 18812 AN: 41462

American (AMR) AF: 0.433 AC: 6617 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3472

East Asian (EAS) AF: 0.810 AC: 4191 AN: 5176

South Asian (SAS) AF: 0.405 AC: 1950 AN: 4816

European-Finnish (FIN) AF: 0.514 AC: 5441 AN: 10576

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34297 AN: 67962

Other (OTH) AF: 0.480 AC: 1011 AN: 2106

Alfa AF: 0.491 Hom.: 50045

Bravo AF: 0.485

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.20
DANN	Benign	0.50
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7753394; hg19: chr6-138085248;