9-34143309-A-G

Variant names:

• chr9-34143309-A-G
• rs4879753

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 0.307 in 149,430 control chromosomes in the GnomAD database, including 7,457 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 0.31 (7457 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.307 AC: 45860 AN: 149342 Hom.: 7452 Cov.: 29

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.307 AC: 45899 AN: 149430 Hom.: 7457 Cov.: 29 AF XY: 0.307 AC XY: 22359 AN XY: 72812

African (AFR) AF: 0.197 AC: 7976 AN: 40464

American (AMR) AF: 0.325 AC: 4862 AN: 14938

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1209 AN: 3458

East Asian (EAS) AF: 0.234 AC: 1175 AN: 5032

South Asian (SAS) AF: 0.285 AC: 1350 AN: 4734

European-Finnish (FIN) AF: 0.378 AC: 3764 AN: 9962

Middle Eastern (MID) AF: 0.344 AC: 97 AN: 282

European-Non Finnish (NFE) AF: 0.362 AC: 24450 AN: 67606

Other (OTH) AF: 0.307 AC: 631 AN: 2058

Alfa AF: 0.332 Hom.: 1396

Bravo AF: 0.294

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4879753; hg19: chr9-34143307;