chr4-54634059-C-A

Position:

• chr4-54634059-C-A

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 0.204 in 152,114 control chromosomes in the GnomAD database, including 3,987 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 0.20 (3987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

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 (AMR) allele frequency at 95% confidence interval = 0.287 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: 0.204 AC: 30963 AN: 151996 Hom.: 3987 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.204 AC: 30963 AN: 152114 Hom.: 3987 Cov.: 32 AF XY: 0.200 AC XY: 14883 AN XY: 74334

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0706

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.218

Alfa AF: 0.269 Hom.: 5604

Bravo AF: 0.205

Asia WGS AF: 0.102 AC: 355 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	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6831020; hg19: chr4-55500226;