rs353873

chr4-166200821-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;