rs1920325

Variant names:

• chr3-104147346-T-C
• rs1920325

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.188 AC: 7818 AN: 41478

American (AMR) AF: 0.278 AC: 4239 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1106 AN: 5154

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3902 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24090 AN: 67906

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.308 Hom.: 1308

Bravo AF: 0.282

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.91
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1920325; hg19: chr3-103866190;