rs489332

Variant names:

• chr9-75413430-C-T
• rs489332
• ENST00000778465.1:n.109+22147C>T

Variant summary

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

The ENST00000778465.1(ENSG00000301354):​n.109+22147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,114 control chromosomes in the GnomAD database, including 3,276 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 0.20 (3276 hom., cov: 32)
• Consequence: ENSG00000301354 ENST00000778465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701
• Publications: 5 publications found

Genes affected

ENSG00000301354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778465.1. 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
	ENSG00000301354	ENST00000778465.1		n.109+22147C>T		intron	N/A
	ENSG00000301354	ENST00000778466.1		n.271+7398C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29979 AN: 151998 Hom.: 3276 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0631

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.197 AC: 30014 AN: 152114 Hom.: 3276 Cov.: 32 AF XY: 0.193 AC XY: 14327 AN XY: 74370

African (AFR) AF: 0.276 AC: 11463 AN: 41468

American (AMR) AF: 0.172 AC: 2630 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.0632 AC: 327 AN: 5174

South Asian (SAS) AF: 0.120 AC: 581 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10594

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12368 AN: 67986

Other (OTH) AF: 0.205 AC: 433 AN: 2114

Alfa AF: 0.187 Hom.: 10456

Bravo AF: 0.203

Asia WGS AF: 0.105 AC: 366 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs489332; hg19: chr9-78028346;