chr9-107866539-T-C

Variant names:

• chr9-107866539-T-C
• rs4978629

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 0.28 in 151,792 control chromosomes in the GnomAD database, including 6,277 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 0.28 (6277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42504 AN: 151674 Hom.: 6263 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.280 AC: 42540 AN: 151792 Hom.: 6277 Cov.: 32 AF XY: 0.291 AC XY: 21578 AN XY: 74198

African (AFR) AF: 0.255 AC: 10581 AN: 41474

American (AMR) AF: 0.358 AC: 5462 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2503 AN: 5150

South Asian (SAS) AF: 0.446 AC: 2149 AN: 4820

European-Finnish (FIN) AF: 0.343 AC: 3549 AN: 10356

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16571 AN: 67946

Other (OTH) AF: 0.271 AC: 570 AN: 2106

Alfa AF: 0.256 Hom.: 11672

Bravo AF: 0.278

Asia WGS AF: 0.430 AC: 1475 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.7
DANN	Benign	0.73
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4978629; hg19: chr9-110628820;