rs1878658

Variant names:

• chr6-137657249-A-G
• rs1878658
• ENST00000746620.1:n.105+9258A>G

Variant summary

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

The ENST00000746620.1(LINC03004):​n.105+9258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,238 control chromosomes in the GnomAD database, including 1,887 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 0.15 (1887 hom., cov: 32)
• Consequence: LINC03004 ENST00000746620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 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	ENST00000746620.1	n.105+9258A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22755 AN: 152120 Hom.: 1890 Cov.: 32

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.149 AC: 22740 AN: 152238 Hom.: 1887 Cov.: 32 AF XY: 0.147 AC XY: 10974 AN XY: 74428

African (AFR) AF: 0.0765 AC: 3180 AN: 41560

American (AMR) AF: 0.182 AC: 2782 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.0939 AC: 487 AN: 5186

South Asian (SAS) AF: 0.185 AC: 895 AN: 4828

European-Finnish (FIN) AF: 0.140 AC: 1482 AN: 10596

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12580 AN: 67998

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.170 Hom.: 559

Bravo AF: 0.151

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.47
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1878658; hg19: chr6-137978386;