chr13-105533454-G-A

Variant names:

• chr13-105533454-G-A
• rs9519707

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 0.455 in 151,908 control chromosomes in the GnomAD database, including 16,526 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 0.45 (16526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.537 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: 0.455 AC: 69050 AN: 151790 Hom.: 16523 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.455 AC: 69069 AN: 151908 Hom.: 16526 Cov.: 32 AF XY: 0.460 AC XY: 34134 AN XY: 74208

African (AFR) AF: 0.298 AC: 12335 AN: 41450

American (AMR) AF: 0.544 AC: 8292 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2712 AN: 5136

South Asian (SAS) AF: 0.555 AC: 2673 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5612 AN: 10518

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34259 AN: 67948

Other (OTH) AF: 0.447 AC: 944 AN: 2112

Alfa AF: 0.485 Hom.: 58440

Bravo AF: 0.446

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9519707; hg19: chr13-106185803;