rs13088205

chr3-12446307-T-G

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 0.338 in 152,054 control chromosomes in the GnomAD database, including 9,647 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 0.34 (9647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.338 AC: 51317 AN: 151936 Hom.: 9645 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.338 AC: 51368 AN: 152054 Hom.: 9647 Cov.: 32 AF XY: 0.335 AC XY: 24917 AN XY: 74330

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.309

Alfa AF: 0.328 Hom.: 1103

Bravo AF: 0.351

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13088205; hg19: chr3-12487806;