rs2807580

chr9-124163828-T-Cchr9-124163828-T-G

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 0.217 in 152,138 control chromosomes in the GnomAD database, including 3,830 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 0.22 (3830 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.217 AC: 32943 AN: 152022 Hom.: 3822 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.217 AC: 32983 AN: 152138 Hom.: 3830 Cov.: 33 AF XY: 0.215 AC XY: 16019 AN XY: 74392

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.230

Alfa AF: 0.199 Hom.: 4878

Bravo AF: 0.222

Asia WGS AF: 0.189 AC: 659 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	0.010
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2807580; hg19: chr9-126926107;