chr3-109888085-C-T

Position:

• chr3-109888085-C-T

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 0.207 in 152,040 control chromosomes in the GnomAD database, including 3,564 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 0.21 (3564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.207 AC: 31509 AN: 151922 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.207 AC: 31522 AN: 152040 Hom.: 3564 Cov.: 32 AF XY: 0.202 AC XY: 15026 AN XY: 74304

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.0682

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.198

Alfa AF: 0.190 Hom.: 1549

Bravo AF: 0.206

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6796720; hg19: chr3-109606932;