rs28361032

Variant names:

• chr6-32005239-A-G
• rs28361032

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 0.301 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.301 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

African (AFR) AF: 0.0913 AC: 3606 AN: 39500

American (AMR) AF: 0.432 AC: 6386 AN: 14766

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1818 AN: 3410

East Asian (EAS) AF: 0.288 AC: 1436 AN: 4982

South Asian (SAS) AF: 0.278 AC: 1240 AN: 4462

European-Finnish (FIN) AF: 0.381 AC: 3767 AN: 9890

Middle Eastern (MID) AF: 0.392 AC: 109 AN: 278

European-Non Finnish (NFE) AF: 0.376 AC: 24362 AN: 64834

Other (OTH) AF: 0.300 AC: 601 AN: 2002

Alfa AF: 0.259 Hom.: 2263

Asia WGS AF: 0.260 AC: 891 AN: 3410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.73
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs28361032; hg19: chr6-31973016;