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 ENST00000635999.1(LINC03004):​n.433+20864A>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 ENST00000635999.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901411	XR_007059789.1	n.163+1761A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+20864A>G		intron_variant	Intron 2 of 2	5
ENSG00000283265	ENST00000637996.1	n.160+1761A>G		intron_variant	Intron 1 of 2	5
LINC03004	ENST00000646621.1	n.601+6299A>G		intron_variant	Intron 4 of 4

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 v4.3

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;