rs9289100

Variant names:

• chr3-118337734-A-G
• rs9289100
• ENST00000482142.5:n.232+158889T>C

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+158889T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,204 control chromosomes in the GnomAD database, including 358 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 0.064 (358 hom., cov: 32)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 0 publications found

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482142.5. 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
	ENSG00000243276	ENST00000482142.5	TSL:5	n.232+158889T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9668 AN: 152086 Hom.: 357 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0636 AC: 9685 AN: 152204 Hom.: 358 Cov.: 32 AF XY: 0.0612 AC XY: 4557 AN XY: 74424

African (AFR) AF: 0.0934 AC: 3879 AN: 41520

American (AMR) AF: 0.0462 AC: 707 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0782 AC: 271 AN: 3466

East Asian (EAS) AF: 0.00889 AC: 46 AN: 5174

South Asian (SAS) AF: 0.0507 AC: 244 AN: 4810

European-Finnish (FIN) AF: 0.0299 AC: 317 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4050 AN: 68006

Other (OTH) AF: 0.0662 AC: 140 AN: 2116

Alfa AF: 0.0626 Hom.: 194

Bravo AF: 0.0663

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9289100;

hg19: chr3-118056581;