rs508214

Variant names:

• chr6-137692528-A-G
• rs508214
• ENST00000635999.1:n.433+18404A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-137692528-A-G
• chr6-137692528-A-T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+18404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,178 control chromosomes in the GnomAD database, including 33,286 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 0.66 (33286 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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.433+18404A>G		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000646621.1	n.601+3839A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99817 AN: 152060 Hom.: 33250 Cov.: 33

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.656 AC: 99900 AN: 152178 Hom.: 33286 Cov.: 33 AF XY: 0.656 AC XY: 48839 AN XY: 74410

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.655

Alfa AF: 0.632 Hom.: 5170

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs508214; hg19: chr6-138013665; COSMIC: COSV60285704;