8-28228571-G-A

Variant names:

• chr8-28228571-G-A
• rs6985069
• ENST00000842508.1:n.219+16428C>T

Variant summary

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

The ENST00000842508.1(ENSG00000309630):​n.219+16428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,022 control chromosomes in the GnomAD database, including 34,882 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 0.67 (34882 hom., cov: 32)
• Consequence: ENSG00000309630 ENST00000842508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 4 publications found

Genes affected

ENSG00000309630 (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 (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842508.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309630	ENST00000842508.1		n.219+16428C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102055 AN: 151904 Hom.: 34870 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.672 AC: 102111 AN: 152022 Hom.: 34882 Cov.: 32 AF XY: 0.670 AC XY: 49772 AN XY: 74296

African (AFR) AF: 0.559 AC: 23157 AN: 41414

American (AMR) AF: 0.608 AC: 9282 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4475 AN: 5174

South Asian (SAS) AF: 0.770 AC: 3715 AN: 4822

European-Finnish (FIN) AF: 0.666 AC: 7037 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49444 AN: 67984

Other (OTH) AF: 0.683 AC: 1442 AN: 2112

Alfa AF: 0.674 Hom.: 5510

Bravo AF: 0.663

Asia WGS AF: 0.776 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6985069; hg19: chr8-28086088;