chr4-59213205-A-T

Variant names:

• chr4-59213205-A-T
• rs1393593

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 0.691 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.769 AC: 31892 AN: 41452

American (AMR) AF: 0.616 AC: 9377 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2366 AN: 3464

East Asian (EAS) AF: 0.607 AC: 3124 AN: 5144

South Asian (SAS) AF: 0.701 AC: 3381 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7322 AN: 10574

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45145 AN: 67934

Other (OTH) AF: 0.687 AC: 1447 AN: 2106

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1393593; hg19: chr4-60078923;