rs6806253

Variant names:

• chr3-128563854-A-G
• rs6806253
• ENST00000662068.1:n.291A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662068.1(ENSG00000286806):​n.291A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,116 control chromosomes in the GnomAD database, including 2,795 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 0.19 (2795 hom., cov: 32)
• Consequence: ENSG00000286806 ENST00000662068.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

Genes affected

ENSG00000286806 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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
ENSG00000286806	ENST00000662068.1	n.291A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28177 AN: 151998 Hom.: 2791 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.185 AC: 28193 AN: 152116 Hom.: 2795 Cov.: 32 AF XY: 0.188 AC XY: 13977 AN XY: 74362

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.187

Alfa AF: 0.179 Hom.: 4137

Bravo AF: 0.188

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6806253; hg19: chr3-128282697;