4-146586311-G-A

Position:

• chr4-146586311-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 0.122 in 152,018 control chromosomes in the GnomAD database, including 1,244 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 0.12 (1244 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.122 AC: 18560 AN: 151900 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.122 AC: 18576 AN: 152018 Hom.: 1244 Cov.: 32 AF XY: 0.118 AC XY: 8779 AN XY: 74294

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0296

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.121

Alfa AF: 0.117 Hom.: 178

Bravo AF: 0.122

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2174304; hg19: chr4-147507463;