rs28611189

chr8-42665191-T-C

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 0.208 in 152,192 control chromosomes in the GnomAD database, including 3,800 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 0.21 (3800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

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 (AFR) allele frequency at 95% confidence interval = 0.327 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: 0.208 AC: 31643 AN: 152074 Hom.: 3801 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31649 AN: 152192 Hom.: 3800 Cov.: 32 AF XY: 0.206 AC XY: 15305 AN XY: 74424

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.182

Alfa AF: 0.202 Hom.: 642

Bravo AF: 0.209

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.5
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28611189; hg19: chr8-42520334;