chr6-52221483-G-A

Variant names:

• chr6-52221483-G-A
• rs7758579

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 0.253 in 152,000 control chromosomes in the GnomAD database, including 5,074 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 (5074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.13
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.253 AC: 38405 AN: 151882 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.253 AC: 38427 AN: 152000 Hom.: 5074 Cov.: 32 AF XY: 0.253 AC XY: 18775 AN XY: 74306

African (AFR) AF: 0.319 AC: 13222 AN: 41428

American (AMR) AF: 0.184 AC: 2806 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1047 AN: 5178

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2306 AN: 10542

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15591 AN: 67968

Other (OTH) AF: 0.257 AC: 542 AN: 2106

Alfa AF: 0.247 Hom.: 601

Bravo AF: 0.251

Asia WGS AF: 0.246 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.052
DANN	Benign	0.62
PhyloP100		-5.1

Splicing

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

Other links and lift over

dbSNP: rs7758579; hg19: chr6-52086281;