3-117480904-T-C

Position:

• chr3-117480904-T-C

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 0.404 in 152,096 control chromosomes in the GnomAD database, including 14,915 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 0.40 (14915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 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: 0.405 AC: 61524 AN: 151978 Hom.: 14921 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.404 AC: 61500 AN: 152096 Hom.: 14915 Cov.: 32 AF XY: 0.399 AC XY: 29626 AN XY: 74324

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.414

Alfa AF: 0.431 Hom.: 3146

Bravo AF: 0.378

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1698041; hg19: chr3-117199751;