rs4466373

Variant names:

• chr8-109073637-C-T
• rs4466373

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 0.219 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.218 AC: 9068 AN: 41522

American (AMR) AF: 0.195 AC: 2982 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2562 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2346 AN: 10582

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13949 AN: 67984

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.214 Hom.: 1588

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4466373; hg19: chr8-110085866;