3-195744621-C-G

Position:

• chr3-195744621-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.36 (34 hom., cov: 48)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.195744621C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 54294 AN: 149812 Hom.: 33 Cov.: 48 FAILED QC

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.380

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.363 AC: 54351 AN: 149930 Hom.: 34 Cov.: 48 AF XY: 0.364 AC XY: 26621 AN XY: 73182

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.381

Alfa AF: 0.155 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.88
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7633103; hg19: chr3-195471492;