chr6-32690139-T-C

Variant names:

• chr6-32690139-T-C
• rs7775055
• ENST00000790899.1:n.216A>G

Variant summary

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

The ENST00000790899.1(ENSG00000302994):​n.216A>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 0.0617 in 132,978 control chromosomes in the GnomAD database, including 319 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 0.062 (319 hom., cov: 30)
• Consequence: ENSG00000302994 ENST00000790899.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 31 publications found

Genes affected

ENSG00000302994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790899.1. 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
	ENSG00000302994	ENST00000790899.1		n.216A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0617 AC: 8192 AN: 132866 Hom.: 318 Cov.: 30

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.0376

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0432

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0553

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

GnomAD4 genome AF: 0.0617 AC: 8210 AN: 132978 Hom.: 319 Cov.: 30 AF XY: 0.0663 AC XY: 4313 AN XY: 65016

African (AFR) AF: 0.0788 AC: 2882 AN: 36584

American (AMR) AF: 0.108 AC: 1464 AN: 13522

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 66 AN: 2834

East Asian (EAS) AF: 0.106 AC: 438 AN: 4142

South Asian (SAS) AF: 0.0198 AC: 64 AN: 3230

European-Finnish (FIN) AF: 0.117 AC: 1177 AN: 10046

Middle Eastern (MID) AF: 0.0458 AC: 12 AN: 262

European-Non Finnish (NFE) AF: 0.0331 AC: 1974 AN: 59684

Other (OTH) AF: 0.0554 AC: 101 AN: 1822

Alfa AF: 0.0457 Hom.: 428

Bravo AF: 0.0561

Asia WGS AF: 0.0510 AC: 177 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7775055; hg19: chr6-32657916;