rs4466373

Variant names:

• chr8-109073637-C-T
• rs4466373

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 0.219 in 152,144 control chromosomes in the GnomAD database, including 3,933 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 0.22 (3933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.220 AC: 33375 AN: 152026 Hom.: 3930 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.219 AC: 33383 AN: 152144 Hom.: 3933 Cov.: 33 AF XY: 0.219 AC XY: 16298 AN XY: 74368

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.198

Alfa AF: 0.202 Hom.: 819

Bravo AF: 0.223

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4466373; hg19: chr8-110085866;