chr6-132572573-G-A

Position:

• chr6-132572573-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.527

Alfa AF: 0.526 Hom.: 20246

Bravo AF: 0.537

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4305745; hg19: chr6-132893712;