rs28367594

chr6-31290364-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 0.0519 in 152,276 control chromosomes in the GnomAD database, including 275 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 0.052 (275 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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 (AFR) allele frequency at 95% confidence interval = 0.0908 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: 0.0519 AC: 7904 AN: 152158 Hom.: 275 Cov.: 33

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0519 AC: 7906 AN: 152276 Hom.: 275 Cov.: 33 AF XY: 0.0503 AC XY: 3742 AN XY: 74460

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0418 Hom.: 79

Bravo AF: 0.0607

Asia WGS AF: 0.0200 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.5
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28367594; hg19: chr6-31258141;