rs7329899

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;