chr3-120526978-C-A

Variant names:

• chr3-120526978-C-A
• rs1259489

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.239 in 152,084 control chromosomes in the GnomAD database, including 4,452 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 0.24 (4452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.238 AC: 36234 AN: 151966 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.239 AC: 36278 AN: 152084 Hom.: 4452 Cov.: 32 AF XY: 0.235 AC XY: 17460 AN XY: 74332

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0510

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.261

Alfa AF: 0.186 Hom.: 565

Bravo AF: 0.237

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1259489; hg19: chr3-120245825;