rs28361032

chr6-32005239-A-G

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 0.301 in 144,946 control chromosomes in the GnomAD database, including 11,468 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 0.30 (11468 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 43647 AN: 144834 Hom.: 11460 Cov.: 29

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.301 AC: 43664 AN: 144946 Hom.: 11468 Cov.: 29 AF XY: 0.302 AC XY: 21365 AN XY: 70658

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.300

Alfa AF: 0.350 Hom.: 2020

Asia WGS AF: 0.260 AC: 891 AN: 3410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.79
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28361032; hg19: chr6-31973016;