chr4-154530607-T-A

Position:

• chr4-154530607-T-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 0.184 in 151,060 control chromosomes in the GnomAD database, including 3,287 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 0.18 (3287 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.184 AC: 27842 AN: 150952 Hom.: 3289 Cov.: 29

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 27841 AN: 151060 Hom.: 3287 Cov.: 29 AF XY: 0.191 AC XY: 14109 AN XY: 73688

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.178

Alfa AF: 0.206 Hom.: 2109

Bravo AF: 0.178

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
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: rs12511469; hg19: chr4-155451759;