9-128439616-A-G

Variant names:

• chr9-128439616-A-G
• rs4837264

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 0.272 in 151,958 control chromosomes in the GnomAD database, including 6,469 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 0.27 (6469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41321 AN: 151840 Hom.: 6441 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.272 AC: 41391 AN: 151958 Hom.: 6469 Cov.: 31 AF XY: 0.273 AC XY: 20304 AN XY: 74278

African (AFR) AF: 0.424 AC: 17549 AN: 41422

American (AMR) AF: 0.222 AC: 3381 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3466

East Asian (EAS) AF: 0.335 AC: 1725 AN: 5150

South Asian (SAS) AF: 0.250 AC: 1202 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2678 AN: 10562

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13732 AN: 67988

Other (OTH) AF: 0.236 AC: 499 AN: 2110

Alfa AF: 0.222 Hom.: 9138

Bravo AF: 0.279

Asia WGS AF: 0.314 AC: 1089 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	1.9
DANN	Benign	0.34
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs4837264; hg19: chr9-131201895;