chr6-132572626-G-A

Variant names:

• chr6-132572626-G-A
• rs4305746

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 0.544 in 151,966 control chromosomes in the GnomAD database, including 22,787 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 0.54 (22787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.544 AC: 82649 AN: 151846 Hom.: 22773 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.544 AC: 82713 AN: 151966 Hom.: 22787 Cov.: 32 AF XY: 0.547 AC XY: 40661 AN XY: 74272

African (AFR) AF: 0.593 AC: 24552 AN: 41416

American (AMR) AF: 0.511 AC: 7799 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2219 AN: 5166

South Asian (SAS) AF: 0.625 AC: 3016 AN: 4826

European-Finnish (FIN) AF: 0.563 AC: 5937 AN: 10544

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35791 AN: 67966

Other (OTH) AF: 0.524 AC: 1103 AN: 2104

Alfa AF: 0.519 Hom.: 13094

Bravo AF: 0.537

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.85
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4305746; hg19: chr6-132893765;