13-79725587-A-G

Variant names:

• chr13-79725587-A-G
• rs2039553

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 0.55 in 151,892 control chromosomes in the GnomAD database, including 23,128 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 0.55 (23128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.550 AC: 83422 AN: 151774 Hom.: 23114 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.550 AC: 83475 AN: 151892 Hom.: 23128 Cov.: 31 AF XY: 0.553 AC XY: 41063 AN XY: 74224

African (AFR) AF: 0.601 AC: 24904 AN: 41416

American (AMR) AF: 0.618 AC: 9437 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1729 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3736 AN: 5164

South Asian (SAS) AF: 0.489 AC: 2349 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5529 AN: 10530

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33959 AN: 67924

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.525 Hom.: 63620

Bravo AF: 0.567

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.4
DANN	Benign	0.84
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2039553; hg19: chr13-80299722;