rs7329434

chr13-70736875-C-T

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 0.332 in 152,046 control chromosomes in the GnomAD database, including 8,814 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 0.33 (8814 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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: 0.332 AC: 50473 AN: 151926 Hom.: 8807 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.332 AC: 50506 AN: 152046 Hom.: 8814 Cov.: 33 AF XY: 0.330 AC XY: 24496 AN XY: 74340

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.327

Alfa AF: 0.352 Hom.: 16326

Bravo AF: 0.321

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7329434; hg19: chr13-71311007;