4-57406362-G-T

Variant names:

• chr4-57406362-G-T
• rs10517393

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.188 AC: 7776 AN: 41448

American (AMR) AF: 0.218 AC: 3335 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1342 AN: 5142

South Asian (SAS) AF: 0.316 AC: 1519 AN: 4810

European-Finnish (FIN) AF: 0.288 AC: 3044 AN: 10574

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15193 AN: 67962

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.219 Hom.: 6384

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
PhyloP100		0.52

Splicing

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

Other links and lift over

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