rs489659

Variant names:

• chr18-7557911-T-C
• rs489659
• ENST00000839922.1:n.167+9929A>G

Variant summary

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

The ENST00000839922.1(ENSG00000309267):​n.167+9929A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,972 control chromosomes in the GnomAD database, including 6,733 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 0.27 (6733 hom., cov: 32)
• Consequence: ENSG00000309267 ENST00000839922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 2 publications found

Genes affected

ENSG00000309267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839922.1. 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
	ENSG00000309267	ENST00000839922.1		n.167+9929A>G		intron	N/A
	ENSG00000309267	ENST00000839923.1		n.132+9929A>G		intron	N/A
	ENSG00000309267	ENST00000839924.1		n.107+9929A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40235 AN: 151852 Hom.: 6715 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.265 AC: 40297 AN: 151972 Hom.: 6733 Cov.: 32 AF XY: 0.271 AC XY: 20132 AN XY: 74282

African (AFR) AF: 0.352 AC: 14593 AN: 41450

American (AMR) AF: 0.346 AC: 5276 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3688 AN: 5118

South Asian (SAS) AF: 0.449 AC: 2153 AN: 4800

European-Finnish (FIN) AF: 0.122 AC: 1294 AN: 10592

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11696 AN: 67970

Other (OTH) AF: 0.260 AC: 548 AN: 2106

Alfa AF: 0.223 Hom.: 3491

Bravo AF: 0.283

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.77
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs489659; hg19: chr18-7557909;