rs353873

Variant names:

• chr4-166200821-C-T
• rs353873

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 0.719 in 152,056 control chromosomes in the GnomAD database, including 40,703 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 0.72 (40703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.719 AC: 109221 AN: 151938 Hom.: 40695 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.719 AC: 109272 AN: 152056 Hom.: 40703 Cov.: 32 AF XY: 0.721 AC XY: 53628 AN XY: 74352

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.711

Alfa AF: 0.769 Hom.: 5698

Bravo AF: 0.695

Asia WGS AF: 0.661 AC: 2299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353873; hg19: chr4-167121973;