rs7329899

Variant names:

• chr13-105826434-G-A
• rs7329899

Your query was ambiguous. Multiple possible variants found:

• chr13-105826434-G-A
• chr13-105826434-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.0964

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.280

Alfa AF: 0.260 Hom.: 2535

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7329899; hg19: chr13-106478783;