4-59343023-T-C

Variant names:

• chr4-59343023-T-C
• rs13102884

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 0.0907 in 151,686 control chromosomes in the GnomAD database, including 820 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 0.091 (820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 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: 0.0907 AC: 13753 AN: 151566 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0907 AC: 13751 AN: 151686 Hom.: 820 Cov.: 32 AF XY: 0.0890 AC XY: 6602 AN XY: 74140

African (AFR) AF: 0.0256 AC: 1061 AN: 41472

American (AMR) AF: 0.0770 AC: 1169 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3466

East Asian (EAS) AF: 0.0449 AC: 231 AN: 5146

South Asian (SAS) AF: 0.0815 AC: 393 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1262 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8896 AN: 67714

Other (OTH) AF: 0.0916 AC: 193 AN: 2106

Alfa AF: 0.110 Hom.: 1259

Bravo AF: 0.0845

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs13102884; hg19: chr4-60208741;