6-137681038-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000646621.1(LINC03004):​n.415-6056C>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 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 66 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000638039.2	n.439-6056C>G		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.415-6056C>G		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.111 AC: 4607 AN: 41496

American (AMR) AF: 0.125 AC: 1916 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 512 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.104 AC: 503 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1867 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14137 AN: 67974

Other (OTH) AF: 0.160 AC: 337 AN: 2110

Alfa AF: 0.0908 Hom.: 145

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6927172; hg19: chr6-138002175;