chr5-13595037-C-T

Variant names:

• chr5-13595037-C-T
• rs184586

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 0.489 in 151,956 control chromosomes in the GnomAD database, including 19,623 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 (19623 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74248 AN: 151836 Hom.: 19589 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.489 AC: 74335 AN: 151956 Hom.: 19623 Cov.: 33 AF XY: 0.493 AC XY: 36584 AN XY: 74268

African (AFR) AF: 0.663 AC: 27471 AN: 41462

American (AMR) AF: 0.365 AC: 5567 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4325 AN: 5178

South Asian (SAS) AF: 0.445 AC: 2146 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4951 AN: 10506

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26926 AN: 67968

Other (OTH) AF: 0.469 AC: 991 AN: 2114

Alfa AF: 0.436 Hom.: 2609

Bravo AF: 0.489

Asia WGS AF: 0.595 AC: 2067 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs184586; hg19: chr5-13595146;