chr9-124163828-T-C

Variant names:

• chr9-124163828-T-C
• rs2807580

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 0.217 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
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.217 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

African (AFR) AF: 0.273 AC: 11332 AN: 41480

American (AMR) AF: 0.221 AC: 3372 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3466

East Asian (EAS) AF: 0.148 AC: 767 AN: 5180

South Asian (SAS) AF: 0.169 AC: 814 AN: 4816

European-Finnish (FIN) AF: 0.198 AC: 2096 AN: 10604

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13119 AN: 67992

Other (OTH) AF: 0.230 AC: 484 AN: 2108

Alfa AF: 0.204 Hom.: 8378

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2807580; hg19: chr9-126926107;