rs28366194

Positions:

• chr6-32414163-A-T

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 0.0878 in 152,262 control chromosomes in the GnomAD database, including 770 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 0.088 (770 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.0878 AC: 13356 AN: 152144 Hom.: 769 Cov.: 30

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0878 AC: 13364 AN: 152262 Hom.: 770 Cov.: 30 AF XY: 0.0845 AC XY: 6289 AN XY: 74460

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.0747

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.0735

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0742 Hom.: 60

Bravo AF: 0.0991

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28366194; hg19: chr6-32381940;