6-28808340-G-A

Variant names:

• chr6-28808340-G-A
• rs4324798
• ENST00000829044.1:n.694+5066G>A

Variant summary

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

The ENST00000829044.1(ENSG00000307816):​n.694+5066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,278 control chromosomes in the GnomAD database, including 470 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 0.070 (470 hom., cov: 32)
• Consequence: ENSG00000307816 ENST00000829044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 87 publications found

Genes affected

ENSG00000307816 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829044.1. 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
	ENSG00000307816	ENST00000829044.1		n.694+5066G>A		intron	N/A
	ENSG00000307816	ENST00000829045.1		n.403+5066G>A		intron	N/A
	ENSG00000307816	ENST00000829046.1		n.280+5066G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10668 AN: 152160 Hom.: 469 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0285

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0701 AC: 10672 AN: 152278 Hom.: 470 Cov.: 32 AF XY: 0.0642 AC XY: 4782 AN XY: 74474

African (AFR) AF: 0.0816 AC: 3388 AN: 41534

American (AMR) AF: 0.0284 AC: 435 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4822

European-Finnish (FIN) AF: 0.0398 AC: 422 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6101 AN: 68026

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0837 Hom.: 2402

Bravo AF: 0.0707

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.72
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs4324798; hg19: chr6-28776117;