ENST00000441381.2:n.426-198C>G

Variant names:

• chr6-29266733-C-G
• rs10484545
• ENST00000441381.2:n.426-198C>G

Variant summary

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

The ENST00000441381.2(LINC03003):​n.426-198C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0789 in 152,026 control chromosomes in the GnomAD database, including 533 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 0.079 (533 hom., cov: 32)
• Consequence: LINC03003 ENST00000441381.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 10 publications found

Genes affected

LINC03003 (HGNC:56126): (long intergenic non-protein coding RNA 3003)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441381.2. 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
	LINC03003	NR_134629.1		n.310-198C>G		intron	N/A
	LINC03003	NR_134630.1		n.80-23393C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03003	ENST00000441381.2	TSL:3	n.426-198C>G		intron	N/A
	LINC03003	ENST00000606648.2	TSL:3	n.196-23393C>G		intron	N/A
	LINC03003	ENST00000733084.1		n.226-23393C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12005 AN: 151908 Hom.: 534 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0820

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

GnomAD4 genome AF: 0.0789 AC: 11999 AN: 152026 Hom.: 533 Cov.: 32 AF XY: 0.0832 AC XY: 6185 AN XY: 74320

African (AFR) AF: 0.0727 AC: 3015 AN: 41484

American (AMR) AF: 0.0672 AC: 1027 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3460

East Asian (EAS) AF: 0.0867 AC: 449 AN: 5178

South Asian (SAS) AF: 0.136 AC: 655 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1399 AN: 10562

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0687 AC: 4663 AN: 67924

Other (OTH) AF: 0.0816 AC: 172 AN: 2108

Alfa AF: 0.0422 Hom.: 42

Bravo AF: 0.0720

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10484545; hg19: chr6-29234510;