9-108406363-G-A

Variant names:

• chr9-108406363-G-A
• rs1886106
• ENST00000826308.1:n.97+10569C>T

Variant summary

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

The ENST00000826308.1(ENSG00000307437):​n.97+10569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,992 control chromosomes in the GnomAD database, including 5,537 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 0.25 (5537 hom., cov: 32)
• Consequence: ENSG00000307437 ENST00000826308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 4 publications found

Genes affected

ENSG00000307437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826308.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307437	ENST00000826308.1		n.97+10569C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38685 AN: 151874 Hom.: 5542 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.254 AC: 38670 AN: 151992 Hom.: 5537 Cov.: 32 AF XY: 0.253 AC XY: 18830 AN XY: 74302

African (AFR) AF: 0.139 AC: 5768 AN: 41456

American (AMR) AF: 0.241 AC: 3683 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3470

East Asian (EAS) AF: 0.0870 AC: 450 AN: 5170

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4812

European-Finnish (FIN) AF: 0.317 AC: 3348 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21445 AN: 67938

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.260 Hom.: 957

Bravo AF: 0.243

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.81
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1886106; hg19: chr9-111168643;