chr13-105826434-G-A

Variant names:

• chr13-105826434-G-A
• rs7329899

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 0.29 in 152,012 control chromosomes in the GnomAD database, including 7,011 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 0.29 (7011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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: 0.290 AC: 44032 AN: 151894 Hom.: 7008 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.290 AC: 44054 AN: 152012 Hom.: 7011 Cov.: 32 AF XY: 0.284 AC XY: 21074 AN XY: 74292

African (AFR) AF: 0.418 AC: 17315 AN: 41422

American (AMR) AF: 0.238 AC: 3634 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5182

South Asian (SAS) AF: 0.0964 AC: 465 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10560

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17877 AN: 67974

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.261 Hom.: 2833

Bravo AF: 0.298

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.57
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs7329899; hg19: chr13-106478783;