4-28766154-G-A

Position:

• chr4-28766154-G-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 0.0697 in 152,004 control chromosomes in the GnomAD database, including 487 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 0.070 (487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0697 AC: 10588 AN: 151886 Hom.: 487 Cov.: 32

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0701

Gnomad ASJ AF: 0.0996

Gnomad EAS AF: 0.0153

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0697 AC: 10588 AN: 152004 Hom.: 487 Cov.: 32 AF XY: 0.0674 AC XY: 5007 AN XY: 74314

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0996

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0815 Hom.: 75

Bravo AF: 0.0716

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11737432; hg19: chr4-28767776;