rs4698169

Positions:

• chr4-17133720-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 0.0885 in 152,204 control chromosomes in the GnomAD database, including 660 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 0.089 (660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0885 AC: 13455 AN: 152086 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.0992

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

GnomAD4 genome AF: 0.0885 AC: 13472 AN: 152204 Hom.: 660 Cov.: 32 AF XY: 0.0897 AC XY: 6673 AN XY: 74404

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0789

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0831 Hom.: 583

Bravo AF: 0.0939

Asia WGS AF: 0.152 AC: 530 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	0.31
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4698169; hg19: chr4-17135343;