6-52233570-A-G

Variant names:

• chr6-52233570-A-G
• rs2064331

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 0.552 in 151,776 control chromosomes in the GnomAD database, including 23,234 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 0.55 (23234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83691 AN: 151656 Hom.: 23211 Cov.: 31

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.552 AC: 83759 AN: 151776 Hom.: 23234 Cov.: 31 AF XY: 0.555 AC XY: 41148 AN XY: 74120

African (AFR) AF: 0.568 AC: 23516 AN: 41400

American (AMR) AF: 0.432 AC: 6584 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2783 AN: 5168

South Asian (SAS) AF: 0.579 AC: 2780 AN: 4800

European-Finnish (FIN) AF: 0.646 AC: 6748 AN: 10450

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37427 AN: 67930

Other (OTH) AF: 0.557 AC: 1175 AN: 2108

Alfa AF: 0.541 Hom.: 28652

Bravo AF: 0.535

Asia WGS AF: 0.510 AC: 1772 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.5
DANN	Benign	0.84
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2064331; hg19: chr6-52098368;