4-146608057-G-A

Position:

• chr4-146608057-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 0.175 in 152,098 control chromosomes in the GnomAD database, including 2,800 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 0.17 (2800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.174 AC: 26515 AN: 151980 Hom.: 2795 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.175 AC: 26543 AN: 152098 Hom.: 2800 Cov.: 32 AF XY: 0.169 AC XY: 12534 AN XY: 74360

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0477

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.169

Alfa AF: 0.135 Hom.: 2006

Bravo AF: 0.182

Asia WGS AF: 0.100 AC: 347 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	2.6
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6835151; hg19: chr4-147529209;