rs6533477

Positions:

• chr4-109907647-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.0455

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.135

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6533477; hg19: chr4-110828803;