rs609438

Variant names:

• chr6-137702105-C-A
• rs609438
• ENST00000635999.1:n.433+27981C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-137702105-C-A
• chr6-137702105-C-G
• chr6-137702105-C-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+27981C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,002 control chromosomes in the GnomAD database, including 25,322 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 0.57 (25322 hom., cov: 31)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 8 publications found

Genes affected

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

ENSG00000303318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+27981C>A		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000646621.1	n.601+13416C>A		intron_variant	Intron 4 of 4
ENSG00000303318	ENST00000793597.1	n.305-2576G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86262 AN: 151884 Hom.: 25300 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.568 AC: 86326 AN: 152002 Hom.: 25322 Cov.: 31 AF XY: 0.572 AC XY: 42522 AN XY: 74300

African (AFR) AF: 0.666 AC: 27596 AN: 41466

American (AMR) AF: 0.558 AC: 8513 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1622 AN: 3466

East Asian (EAS) AF: 0.961 AC: 4982 AN: 5182

South Asian (SAS) AF: 0.505 AC: 2426 AN: 4808

European-Finnish (FIN) AF: 0.577 AC: 6088 AN: 10558

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33337 AN: 67946

Other (OTH) AF: 0.569 AC: 1200 AN: 2110

Alfa AF: 0.528 Hom.: 33033

Bravo AF: 0.571

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs609438; hg19: chr6-138023242;