6-139481094-G-C

Variant names:

• chr6-139481094-G-C
• rs3010294
• ENST00000650173.1:n.1279-25370G>C

Variant summary

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

The ENST00000650173.1(ENSG00000226571):​n.1279-25370G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,212 control chromosomes in the GnomAD database, including 53,399 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 0.84 (53399 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000650173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850
• Publications: 3 publications found

Genes affected

ENSG00000226571 (HGNC:):

LINC01625 (HGNC:52052): (long intergenic non-protein coding RNA 1625)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 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
ENSG00000226571	ENST00000650173.1	n.1279-25370G>C		intron_variant	Intron 7 of 7
ENSG00000226571	ENST00000775574.1	n.193+29425G>C		intron_variant	Intron 2 of 2
ENSG00000226571	ENST00000775576.1	n.375+23338G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127208 AN: 152096 Hom.: 53359 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.836 AC: 127304 AN: 152212 Hom.: 53399 Cov.: 32 AF XY: 0.836 AC XY: 62184 AN XY: 74402

African (AFR) AF: 0.787 AC: 32687 AN: 41516

American (AMR) AF: 0.855 AC: 13074 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3131 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3866 AN: 5170

South Asian (SAS) AF: 0.759 AC: 3665 AN: 4828

European-Finnish (FIN) AF: 0.904 AC: 9577 AN: 10598

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58501 AN: 68026

Other (OTH) AF: 0.840 AC: 1775 AN: 2112

Alfa AF: 0.853 Hom.: 6889

Bravo AF: 0.832

Asia WGS AF: 0.741 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.9
DANN	Benign	0.37
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs3010294; hg19: chr6-139802231;