rs6910534

Variant names:

• chr6-108734251-C-G
• rs6910534
• ENST00000720494.1:n.246+3174C>G

Variant summary

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

The ENST00000720494.1(LINC00222):​n.246+3174C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,144 control chromosomes in the GnomAD database, including 1,529 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 0.13 (1529 hom., cov: 33)
• Consequence: LINC00222 ENST00000720494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 5 publications found

Genes affected

LINC00222 (HGNC:21560): (long intergenic non-protein coding RNA 222)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720494.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00222	ENST00000720494.1		n.246+3174C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19835 AN: 152026 Hom.: 1525 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.131 AC: 19860 AN: 152144 Hom.: 1529 Cov.: 33 AF XY: 0.132 AC XY: 9827 AN XY: 74382

African (AFR) AF: 0.212 AC: 8790 AN: 41490

American (AMR) AF: 0.131 AC: 2001 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3472

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5184

South Asian (SAS) AF: 0.105 AC: 507 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1605 AN: 10582

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0912 AC: 6202 AN: 67998

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.126 Hom.: 166

Bravo AF: 0.130

Asia WGS AF: 0.0700 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6910534;

hg19: chr6-109055454;