3-107988906-T-G

Position:

• chr3-107988906-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 0.763 in 152,180 control chromosomes in the GnomAD database, including 44,788 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 0.76 (44788 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116046 AN: 152062 Hom.: 44729 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.763 AC: 116169 AN: 152180 Hom.: 44788 Cov.: 33 AF XY: 0.767 AC XY: 57033 AN XY: 74390

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.769

Alfa AF: 0.726 Hom.: 58919

Bravo AF: 0.761

Asia WGS AF: 0.905 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.18
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs697957; hg19: chr3-107707753;