6-137681038-C-G

Variant names:

• chr6-137681038-C-G
• rs6927172
• ENST00000635999.1:n.433+6914C>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000635999.1(LINC03004):​n.433+6914C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,104 control chromosomes in the GnomAD database, including 2,104 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 0.16 (2104 hom., cov: 30)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+6914C>G		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.1	n.439-6056C>G		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.415-6056C>G		intron_variant	Intron 2 of 4
LINC03004	ENST00000666119.1	n.393-6056C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24058 AN: 151986 Hom.: 2102 Cov.: 30

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 24071 AN: 152104 Hom.: 2104 Cov.: 30 AF XY: 0.154 AC XY: 11424 AN XY: 74346

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.160

Alfa AF: 0.0409 Hom.: 44

Bravo AF: 0.152

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6927172; hg19: chr6-138002175;