rs13318232

chr3-114092841-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0778 in 152,130 control chromosomes in the GnomAD database, including 521 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 0.078 (521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.088 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: 0.0779 AC: 11839 AN: 152012 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0778 AC: 11842 AN: 152130 Hom.: 521 Cov.: 32 AF XY: 0.0766 AC XY: 5698 AN XY: 74374

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.0449

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0873 Hom.: 830

Bravo AF: 0.0799

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	20
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13318232; hg19: chr3-113811688;