rs74566133

Variant names:

• chr8-133766099-C-T
• rs74566133

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0258 in 152,276 control chromosomes in the GnomAD database, including 86 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 0.026 (86 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0258 (3926/152276) while in subpopulation NFE AF= 0.0339 (2305/68026). AF 95% confidence interval is 0.0327. There are 86 homozygotes in gnomad4. There are 2045 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 86 gene

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: 0.0258 AC: 3925 AN: 152158 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00627

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0258 AC: 3926 AN: 152276 Hom.: 86 Cov.: 32 AF XY: 0.0275 AC XY: 2045 AN XY: 74448

Gnomad4 AFR AF: 0.00625

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0280 Hom.: 11

Bravo AF: 0.0211

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74566133; hg19: chr8-134778342;