9-134245399-T-C

Variant names:

• chr9-134245399-T-C
• rs4917360

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 0.735 in 152,202 control chromosomes in the GnomAD database, including 41,327 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 0.74 (41327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.798 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: 0.735 AC: 111816 AN: 152084 Hom.: 41290 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.735 AC: 111911 AN: 152202 Hom.: 41327 Cov.: 33 AF XY: 0.740 AC XY: 55040 AN XY: 74400

African (AFR) AF: 0.792 AC: 32886 AN: 41536

American (AMR) AF: 0.810 AC: 12396 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3706 AN: 5164

South Asian (SAS) AF: 0.773 AC: 3736 AN: 4834

European-Finnish (FIN) AF: 0.689 AC: 7301 AN: 10590

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46695 AN: 67986

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.708 Hom.: 138377

Bravo AF: 0.745

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.24
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4917360; hg19: chr9-137137245;