4-54368658-C-G

Variant names:

• chr4-54368658-C-G
• rs17690232

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 0.142 in 152,070 control chromosomes in the GnomAD database, including 1,794 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 0.14 (1794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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: 0.142 AC: 21574 AN: 151952 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.142 AC: 21575 AN: 152070 Hom.: 1794 Cov.: 32 AF XY: 0.139 AC XY: 10337 AN XY: 74322

Gnomad4 AFR AF: 0.0771

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00523

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.148

Alfa AF: 0.165 Hom.: 1256

Bravo AF: 0.135

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17690232; hg19: chr4-55234825;