ENST00000635999.1:n.434-8801T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635999.1(LINC03004):​n.434-8801T>C 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: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC03004	ENST00000635999.1	n.434-8801T>C		intron_variant	Intron 2 of 2	5
LINC02539	ENST00000645996.1	n.214-24419A>G		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.553

Alfa AF: 0.509 Hom.: 26864

Bravo AF: 0.567

Asia WGS AF: 0.662 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6927210; hg19: chr6-138076153;