rs1920325

Positions:

• chr3-104147346-T-C

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 0.293 in 151,960 control chromosomes in the GnomAD database, including 6,949 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 0.29 (6949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 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: 0.294 AC: 44574 AN: 151842 Hom.: 6949 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.293 AC: 44600 AN: 151960 Hom.: 6949 Cov.: 32 AF XY: 0.296 AC XY: 21993 AN XY: 74284

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.291

Alfa AF: 0.312 Hom.: 1294

Bravo AF: 0.282

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.91
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920325; hg19: chr3-103866190;