13-46829225-A-G

Variant names:

• chr13-46829225-A-G
• rs7333412

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 0.3 in 152,172 control chromosomes in the GnomAD database, including 7,971 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 0.30 (7971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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: 0.300 AC: 45660 AN: 152054 Hom.: 7961 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.300 AC: 45719 AN: 152172 Hom.: 7971 Cov.: 32 AF XY: 0.296 AC XY: 22047 AN XY: 74414

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.294

Alfa AF: 0.237 Hom.: 9001

Bravo AF: 0.321

Asia WGS AF: 0.201 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7333412; hg19: chr13-47403360;