6-3057179-A-G

Variant names:

• chr6-3057179-A-G
• rs7775816
• ENST00000433761.2:n.854A>G

Variant summary

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

The ENST00000433761.2(ENSG00000229282):​n.854A>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 0.767 in 152,180 control chromosomes in the GnomAD database, including 45,353 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 0.77 (45353 hom., cov: 32)
• Consequence: ENSG00000229282 ENST00000433761.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 14 publications found

Genes affected

ENSG00000229282 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433761.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229282	ENST00000433761.2	TSL:2	n.854A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000229282	ENST00000817020.1		n.*141A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116578 AN: 152060 Hom.: 45318 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.767 AC: 116664 AN: 152180 Hom.: 45353 Cov.: 32 AF XY: 0.766 AC XY: 56990 AN XY: 74404

African (AFR) AF: 0.658 AC: 27295 AN: 41496

American (AMR) AF: 0.710 AC: 10842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2600 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3490 AN: 5176

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4830

European-Finnish (FIN) AF: 0.876 AC: 9287 AN: 10600

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57179 AN: 68010

Other (OTH) AF: 0.738 AC: 1558 AN: 2112

Alfa AF: 0.809 Hom.: 219206

Bravo AF: 0.750

Asia WGS AF: 0.671 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.86
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7775816; hg19: chr6-3057413;