4-10322536-G-A

Variant names:

• chr4-10322536-G-A
• rs9291683

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 0.426 in 151,976 control chromosomes in the GnomAD database, including 14,098 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 0.43 (14098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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: 0.427 AC: 64775 AN: 151858 Hom.: 14097 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.426 AC: 64789 AN: 151976 Hom.: 14098 Cov.: 32 AF XY: 0.426 AC XY: 31641 AN XY: 74292

African (AFR) AF: 0.337 AC: 13947 AN: 41434

American (AMR) AF: 0.407 AC: 6221 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3466

East Asian (EAS) AF: 0.293 AC: 1515 AN: 5164

South Asian (SAS) AF: 0.542 AC: 2610 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4854 AN: 10550

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32439 AN: 67954

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.455 Hom.: 53120

Bravo AF: 0.418

Asia WGS AF: 0.432 AC: 1500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9291683; hg19: chr4-10324160;