chr3-188045610-C-T

Position:

• chr3-188045610-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 0.306 in 151,872 control chromosomes in the GnomAD database, including 7,786 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 0.31 (7786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.306 AC: 46408 AN: 151752 Hom.: 7770 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46459 AN: 151872 Hom.: 7786 Cov.: 31 AF XY: 0.301 AC XY: 22365 AN XY: 74234

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.281

Alfa AF: 0.265 Hom.: 5570

Bravo AF: 0.306

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6789987; hg19: chr3-187763398;