chr4-17133720-C-T

Variant names:

• chr4-17133720-C-T
• rs4698169

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;