rs689566

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376235	XR_930270.3	n.144+2022C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228714	ENST00000646338.1	n.275+142331G>T		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.00404

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.00321

Gnomad4 OTH AF: 0.0341

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689566; hg19: chr9-118361410;