chr4-109907647-A-G

Variant names:

• chr4-109907647-A-G
• rs6533477

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 0.151 in 152,206 control chromosomes in the GnomAD database, including 3,003 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 0.15 (3003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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: 0.151 AC: 22928 AN: 152088 Hom.: 2990 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.0455

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152206 Hom.: 3003 Cov.: 33 AF XY: 0.150 AC XY: 11169 AN XY: 74418

African (AFR) AF: 0.348 AC: 14415 AN: 41470

American (AMR) AF: 0.115 AC: 1763 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5180

South Asian (SAS) AF: 0.0883 AC: 426 AN: 4824

European-Finnish (FIN) AF: 0.0455 AC: 484 AN: 10628

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0590 AC: 4013 AN: 68022

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.121 Hom.: 299

Bravo AF: 0.165

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.71
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6533477; hg19: chr4-110828803;