9-99087445-G-T

Variant names:

• chr9-99087445-G-T
• rs4743325

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 0.252 in 152,102 control chromosomes in the GnomAD database, including 5,418 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 0.25 (5418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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: 0.252 AC: 38372 AN: 151984 Hom.: 5415 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.252 AC: 38390 AN: 152102 Hom.: 5418 Cov.: 32 AF XY: 0.256 AC XY: 19007 AN XY: 74350

African (AFR) AF: 0.247 AC: 10268 AN: 41496

American (AMR) AF: 0.308 AC: 4704 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3114 AN: 5172

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4812

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10594

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14825 AN: 67976

Other (OTH) AF: 0.281 AC: 592 AN: 2108

Alfa AF: 0.238 Hom.: 761

Bravo AF: 0.264

Asia WGS AF: 0.488 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4743325; hg19: chr9-101849727; COSMIC: COSV60380909;