4-59213205-A-T

Variant names:

• chr4-59213205-A-T
• rs1393593

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 0.691 in 151,926 control chromosomes in the GnomAD database, including 36,500 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 0.69 (36500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.690 AC: 104816 AN: 151810 Hom.: 36444 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.691 AC: 104926 AN: 151926 Hom.: 36500 Cov.: 32 AF XY: 0.691 AC XY: 51296 AN XY: 74250

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.687

Alfa AF: 0.681 Hom.: 4408

Bravo AF: 0.684

Asia WGS AF: 0.715 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
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: rs1393593; hg19: chr4-60078923;