rs28361032

Variant names:

• chr6-32005239-A-G
• rs28361032

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;