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. The variant received -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
• Publications: 8 publications found

Genes affected

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635999.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.433+18404A>G		intron	N/A
	LINC03004	ENST00000646621.1		n.601+3839A>G		intron	N/A

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

African (AFR) AF: 0.762 AC: 31648 AN: 41536

American (AMR) AF: 0.624 AC: 9534 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4179 AN: 5182

South Asian (SAS) AF: 0.540 AC: 2606 AN: 4822

European-Finnish (FIN) AF: 0.650 AC: 6883 AN: 10586

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41286 AN: 67976

Other (OTH) AF: 0.655 AC: 1385 AN: 2114

Alfa AF: 0.636 Hom.: 5391

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

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

Other links and lift over

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