rs525977

Variant names:

• chr6-137664515-G-A
• rs525977
• ENST00000642830.1:n.172-1131G>A

Variant summary

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

The ENST00000642830.1(LINC03004):​n.172-1131G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642830.1. 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	ENST00000642830.1		n.172-1131G>A		intron	N/A
	LINC03004	ENST00000691587.2		n.220-1131G>A		intron	N/A
	LINC03004	ENST00000692965.3		n.195-1131G>A		intron	N/A

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

African (AFR) AF: 0.584 AC: 24195 AN: 41440

American (AMR) AF: 0.513 AC: 7831 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2366 AN: 5184

South Asian (SAS) AF: 0.511 AC: 2463 AN: 4824

European-Finnish (FIN) AF: 0.448 AC: 4725 AN: 10538

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35350 AN: 67974

Other (OTH) AF: 0.511 AC: 1078 AN: 2108

Alfa AF: 0.524 Hom.: 5454

Bravo AF: 0.540

Asia WGS AF: 0.439 AC: 1525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.69
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs525977; hg19: chr6-137985652;