4-57406362-G-T

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 0.222 in 151,982 control chromosomes in the GnomAD database, including 3,893 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 0.22 (3893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 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: 0.222 AC: 33753 AN: 151864 Hom.: 3895 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.222 AC: 33764 AN: 151982 Hom.: 3893 Cov.: 32 AF XY: 0.228 AC XY: 16943 AN XY: 74284

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.240

Alfa AF: 0.219 Hom.: 5113

Bravo AF: 0.212

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.8
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517393; hg19: chr4-58272528; COSMIC: COSV56989617;