rs6806253

chr3-128563854-A-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: ENST00000662068.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662068.1	n.291A>G		non_coding_transcript_exon_variant	2/2

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;