3-103285628-A-G

Variant names:

• chr3-103285628-A-G
• rs1907878

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 0.152 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0763 Hom.: 119

Bravo AF: 0.161

Asia WGS AF: 0.130 AC: 455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1907878; hg19: chr3-103004472;