chr8-53252812-G-C

Variant names:

• chr8-53252812-G-C
• rs34418807

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 0.0455 in 152,288 control chromosomes in the GnomAD database, including 187 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 0.045 (187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0454 AC: 6911 AN: 152170 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0455 AC: 6923 AN: 152288 Hom.: 187 Cov.: 32 AF XY: 0.0435 AC XY: 3239 AN XY: 74466

African (AFR) AF: 0.0679 AC: 2823 AN: 41562

American (AMR) AF: 0.0288 AC: 441 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4822

European-Finnish (FIN) AF: 0.0187 AC: 198 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0456 AC: 3100 AN: 68024

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.00870 Hom.: 3

Bravo AF: 0.0469

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.11
DANN	Benign	0.58
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs34418807; hg19: chr8-54165372;