3-103285628-A-G

Variant names:

• chr3-103285628-A-G
• rs1907878

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 0.152 in 152,124 control chromosomes in the GnomAD database, including 2,090 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 0.15 (2090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.152 AC: 23152 AN: 152006 Hom.: 2082 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.152 AC: 23188 AN: 152124 Hom.: 2090 Cov.: 32 AF XY: 0.150 AC XY: 11171 AN XY: 74376

African (AFR) AF: 0.238 AC: 9851 AN: 41476

American (AMR) AF: 0.138 AC: 2115 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.0256 AC: 133 AN: 5186

South Asian (SAS) AF: 0.175 AC: 844 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1135 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8082 AN: 67984

Other (OTH) AF: 0.153 AC: 322 AN: 2108

Alfa AF: 0.0811 Hom.: 142

Bravo AF: 0.161

Asia WGS AF: 0.130 AC: 455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.57
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1907878; hg19: chr3-103004472;