rs13318232

Variant names:

• chr3-114092841-A-G
• rs13318232

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0727 AC: 3017 AN: 41498

American (AMR) AF: 0.0641 AC: 977 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.0449 AC: 233 AN: 5186

South Asian (SAS) AF: 0.0610 AC: 294 AN: 4818

European-Finnish (FIN) AF: 0.0518 AC: 549 AN: 10590

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0899 AC: 6114 AN: 67998

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0868 Hom.: 1035

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
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs13318232; hg19: chr3-113811688;