rs352416

Variant names:

• chr8-28595282-C-A
• rs352416

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.509 AC: 21080 AN: 41432

American (AMR) AF: 0.0626 AC: 956 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.00518 AC: 25 AN: 4830

European-Finnish (FIN) AF: 0.0125 AC: 133 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1077 AN: 68016

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.0692 Hom.: 2439

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs352416; hg19: chr8-28452799;