chr9-96787167-A-G

Variant names:

• chr9-96787167-A-G
• rs4344199

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 0.134 in 152,054 control chromosomes in the GnomAD database, including 3,317 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 0.13 (3317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20263 AN: 151936 Hom.: 3283 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.134 AC: 20339 AN: 152054 Hom.: 3317 Cov.: 32 AF XY: 0.134 AC XY: 9988 AN XY: 74342

African (AFR) AF: 0.385 AC: 15933 AN: 41408

American (AMR) AF: 0.0677 AC: 1034 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3464

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5156

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4820

European-Finnish (FIN) AF: 0.0456 AC: 484 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1030 AN: 68010

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0929 Hom.: 375

Bravo AF: 0.147

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.55
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4344199; hg19: chr9-99549449;