rs667520

chr6-137694988-A-Gchr6-137694988-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+20864A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901411	XR_007059789.1	n.163+1761A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+20864A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000637996.1	n.160+1761A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+6299A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.519

Alfa AF: 0.470 Hom.: 5456

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667520; hg19: chr6-138016125;