rs689566

Variant names:

• chr9-115599131-C-A
• rs689566
• ENST00000646338.1:n.275+142331G>T

Variant summary

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

The ENST00000646338.1(ENSG00000228714):​n.275+142331G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 152,266 control chromosomes in the GnomAD database, including 500 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 0.030 (500 hom., cov: 32)
• Consequence: ENSG00000228714 ENST00000646338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 2 publications found

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646338.1. 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
	ENSG00000228714	ENST00000646338.1		n.275+142331G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4567 AN: 152148 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.00405

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0300 AC: 4566 AN: 152266 Hom.: 500 Cov.: 32 AF XY: 0.0367 AC XY: 2732 AN XY: 74450

African (AFR) AF: 0.00404 AC: 168 AN: 41574

American (AMR) AF: 0.0752 AC: 1149 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2008 AN: 5168

South Asian (SAS) AF: 0.0661 AC: 319 AN: 4824

European-Finnish (FIN) AF: 0.0578 AC: 613 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00321 AC: 218 AN: 68014

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0127 Hom.: 13

Bravo AF: 0.0325

Asia WGS AF: 0.193 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.6
DANN	Benign	0.33
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs689566; hg19: chr9-118361410;