rs352416

chr8-28595282-C-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 0.155 in 152,150 control chromosomes in the GnomAD database, including 5,541 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 0.16 (5541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.155 AC: 23552 AN: 152032 Hom.: 5521 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.155 AC: 23624 AN: 152150 Hom.: 5541 Cov.: 32 AF XY: 0.149 AC XY: 11108 AN XY: 74414

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0522 Hom.: 1286

Bravo AF: 0.174

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.49
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352416; hg19: chr8-28452799;