chr3-117453486-C-A

Variant names:

• chr3-117453486-C-A
• rs10511371

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 0.0982 in 152,126 control chromosomes in the GnomAD database, including 1,638 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 0.098 (1638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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: 0.0981 AC: 14912 AN: 152008 Hom.: 1635 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0982 AC: 14943 AN: 152126 Hom.: 1638 Cov.: 32 AF XY: 0.0977 AC XY: 7267 AN XY: 74388

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.0739

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.0622

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0896

Alfa AF: 0.0356 Hom.: 235

Bravo AF: 0.109

Asia WGS AF: 0.0900 AC: 311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511371; hg19: chr3-117172333;