8-9928984-A-G

Variant names:

• chr8-9928984-A-G
• rs586123
• ENST00000843628.1:n.97+9847A>G

Variant summary

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

The ENST00000843628.1(ENSG00000309740):​n.97+9847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,282 control chromosomes in the GnomAD database, including 58,813 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 0.88 (58813 hom., cov: 33)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 3 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309740	ENST00000843628.1	n.97+9847A>G		intron_variant	Intron 1 of 2
ENSG00000309740	ENST00000843630.1	n.169+9847A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133673 AN: 152164 Hom.: 58777 Cov.: 33

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.878 AC: 133765 AN: 152282 Hom.: 58813 Cov.: 33 AF XY: 0.876 AC XY: 65240 AN XY: 74454

African (AFR) AF: 0.910 AC: 37826 AN: 41566

American (AMR) AF: 0.860 AC: 13163 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3194 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4285 AN: 5184

South Asian (SAS) AF: 0.883 AC: 4260 AN: 4826

European-Finnish (FIN) AF: 0.806 AC: 8542 AN: 10592

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59560 AN: 68024

Other (OTH) AF: 0.877 AC: 1855 AN: 2114

Alfa AF: 0.878 Hom.: 90155

Bravo AF: 0.880

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.28
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs586123; hg19: chr8-9786494;