6-132572573-G-A

Variant names:

• chr6-132572573-G-A
• rs4305745

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 151,926 control chromosomes in the GnomAD database, including 22,772 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 (22772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.544 AC: 82612 AN: 151808 Hom.: 22758 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.544 AC: 82676 AN: 151926 Hom.: 22772 Cov.: 32 AF XY: 0.547 AC XY: 40654 AN XY: 74256

African (AFR) AF: 0.593 AC: 24550 AN: 41412

American (AMR) AF: 0.511 AC: 7792 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1628 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2215 AN: 5158

South Asian (SAS) AF: 0.625 AC: 3013 AN: 4822

European-Finnish (FIN) AF: 0.562 AC: 5938 AN: 10558

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

European-Non Finnish (NFE) AF: 0.526 AC: 35758 AN: 67934

Other (OTH) AF: 0.527 AC: 1111 AN: 2110

Alfa AF: 0.528 Hom.: 25616

Bravo AF: 0.537

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4305745; hg19: chr6-132893712;