rs2279989

chr9-1041524-G-A

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 0.0629 in 152,226 control chromosomes in the GnomAD database, including 333 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 0.063 (333 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9576 AN: 152108 Hom.: 333 Cov.: 33

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0629 AC: 9570 AN: 152226 Hom.: 333 Cov.: 33 AF XY: 0.0630 AC XY: 4691 AN XY: 74430

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.0696

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0743 Hom.: 596

Bravo AF: 0.0582

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.89
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2279989; hg19: chr9-1041524;