chr6-52185555-A-G

Variant names:

• chr6-52185555-A-G
• rs4711998

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 0.633 in 151,988 control chromosomes in the GnomAD database, including 32,251 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 0.63 (32251 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 81 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 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: 0.634 AC: 96234 AN: 151870 Hom.: 32237 Cov.: 30

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.633 AC: 96279 AN: 151988 Hom.: 32251 Cov.: 30 AF XY: 0.630 AC XY: 46797 AN XY: 74304

African (AFR) AF: 0.440 AC: 18240 AN: 41430

American (AMR) AF: 0.719 AC: 10981 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2656 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5172

South Asian (SAS) AF: 0.569 AC: 2732 AN: 4804

European-Finnish (FIN) AF: 0.715 AC: 7560 AN: 10568

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50590 AN: 67958

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.709 Hom.: 72297

Bravo AF: 0.628

Asia WGS AF: 0.441 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4711998; hg19: chr6-52050353;