5-13590417-C-G

Variant names:

• chr5-13590417-C-G
• rs183495

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 0.49 in 152,048 control chromosomes in the GnomAD database, including 19,661 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 0.49 (19661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.489 AC: 74359 AN: 151930 Hom.: 19626 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.490 AC: 74447 AN: 152048 Hom.: 19661 Cov.: 32 AF XY: 0.493 AC XY: 36639 AN XY: 74332

African (AFR) AF: 0.663 AC: 27467 AN: 41454

American (AMR) AF: 0.368 AC: 5625 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1678 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4325 AN: 5172

South Asian (SAS) AF: 0.445 AC: 2148 AN: 4822

European-Finnish (FIN) AF: 0.470 AC: 4960 AN: 10556

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.396 AC: 26932 AN: 67980

Other (OTH) AF: 0.472 AC: 997 AN: 2112

Alfa AF: 0.447 Hom.: 1970

Bravo AF: 0.490

Asia WGS AF: 0.596 AC: 2073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.094
DANN	Benign	0.71
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs183495; hg19: chr5-13590526;