4-28659234-T-C

Position:

• chr4-28659234-T-C

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 0.798 in 152,184 control chromosomes in the GnomAD database, including 48,587 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 0.80 (48587 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.798 AC: 121294 AN: 152066 Hom.: 48551 Cov.: 34

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.798 AC: 121386 AN: 152184 Hom.: 48587 Cov.: 34 AF XY: 0.800 AC XY: 59534 AN XY: 74396

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.804

Alfa AF: 0.810 Hom.: 47901

Bravo AF: 0.793

Asia WGS AF: 0.913 AC: 3168 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9996729; hg19: chr4-28660856;