rs9289678

Variant names:

• chr3-144588254-T-C
• rs9289678

Variant summary

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

The variant allele was found at a frequency of 0.342 in 152,044 control chromosomes in the GnomAD database, including 10,479 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 0.34 (10479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51999 AN: 151926 Hom.: 10468 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.342 AC: 52018 AN: 152044 Hom.: 10479 Cov.: 32 AF XY: 0.346 AC XY: 25683 AN XY: 74296

African (AFR) AF: 0.127 AC: 5260 AN: 41526

American (AMR) AF: 0.362 AC: 5529 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5160

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5523 AN: 10548

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29890 AN: 67936

Other (OTH) AF: 0.350 AC: 740 AN: 2116

Alfa AF: 0.404 Hom.: 22338

Bravo AF: 0.323

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.46
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9289678; hg19: chr3-144307096;