rs28891406

Variant names:

• chr6-32672559-G-A
• rs28891406

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 0.197 in 147,624 control chromosomes in the GnomAD database, including 4,062 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 0.20 (4062 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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: 0.197 AC: 28997 AN: 147506 Hom.: 4067 Cov.: 29

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.197 AC: 29015 AN: 147624 Hom.: 4062 Cov.: 29 AF XY: 0.194 AC XY: 14003 AN XY: 72036

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.191

Alfa AF: 0.184 Hom.: 2535

Asia WGS AF: 0.338 AC: 1159 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28891406; hg19: chr6-32640336;