rs525977

chr6-137664515-G-A

Variant summary

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

The ENST00000642830.1(LINC03004):n.172-1131G>A 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 0.532 in 152,016 control chromosomes in the GnomAD database, including 21,494 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 0.53 (21494 hom., cov: 32)
• Consequence: LINC03004 ENST00000642830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000642830.1	n.172-1131G>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000691587.1	n.39-1131G>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000692965.2	n.172-1131G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80762 AN: 151898 Hom.: 21469 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.532 AC: 80825 AN: 152016 Hom.: 21494 Cov.: 32 AF XY: 0.526 AC XY: 39108 AN XY: 74294

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.511

Alfa AF: 0.522 Hom.: 4670

Bravo AF: 0.540

Asia WGS AF: 0.439 AC: 1525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.26
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs525977; hg19: chr6-137985652;