8-53252812-G-C

Position:

• chr8-53252812-G-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 0.0455 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0454 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

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0288

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0407

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34418807; hg19: chr8-54165372;