rs667520

Variant names:

• chr6-137694988-A-G
• rs667520
• ENST00000635999.1:n.433+20864A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-137694988-A-G
• chr6-137694988-A-T

Variant summary

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

The ENST00000646621.1(LINC03004):​n.601+6299A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,032 control chromosomes in the GnomAD database, including 22,221 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 0.52 (22221 hom., cov: 32)
• Consequence: LINC03004 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 publications found

Genes affected

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

ENSG00000283265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646621.1. 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.433+20864A>G		intron	N/A
	ENSG00000283265	ENST00000637996.1	TSL:5	n.160+1761A>G		intron	N/A
	LINC03004	ENST00000646621.1		n.601+6299A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79044 AN: 151914 Hom.: 22184 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.520 AC: 79129 AN: 152032 Hom.: 22221 Cov.: 32 AF XY: 0.524 AC XY: 38924 AN XY: 74304

African (AFR) AF: 0.724 AC: 30030 AN: 41480

American (AMR) AF: 0.510 AC: 7791 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4154 AN: 5166

South Asian (SAS) AF: 0.436 AC: 2105 AN: 4826

European-Finnish (FIN) AF: 0.473 AC: 4989 AN: 10542

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27227 AN: 67960

Other (OTH) AF: 0.519 AC: 1093 AN: 2106

Alfa AF: 0.478 Hom.: 6200

Bravo AF: 0.531

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs667520; hg19: chr6-138016125;