chr9-6210099-T-C

Variant names:

• chr9-6210099-T-C
• rs3939286

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 0.696 in 151,954 control chromosomes in the GnomAD database, including 37,813 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 0.70 (37813 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 59 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 = 0.937 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: 0.696 AC: 105706 AN: 151836 Hom.: 37800 Cov.: 30

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.696 AC: 105764 AN: 151954 Hom.: 37813 Cov.: 30 AF XY: 0.696 AC XY: 51709 AN XY: 74252

African (AFR) AF: 0.532 AC: 22014 AN: 41394

American (AMR) AF: 0.765 AC: 11686 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4954 AN: 5162

South Asian (SAS) AF: 0.763 AC: 3684 AN: 4826

European-Finnish (FIN) AF: 0.741 AC: 7820 AN: 10550

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51025 AN: 67972

Other (OTH) AF: 0.702 AC: 1481 AN: 2110

Alfa AF: 0.735 Hom.: 63193

Bravo AF: 0.688

Asia WGS AF: 0.817 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3939286; hg19: chr9-6210099;