rs3902354

Variant names:

• chr1-109276674-C-A
• rs3902354

Your query was ambiguous. Multiple possible variants found:

• chr1-109276674-C-A
• chr1-109276674-C-T

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 0.55 in 151,856 control chromosomes in the GnomAD database, including 26,718 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 0.55 (26718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 20 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 (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.550 AC: 83446 AN: 151738 Hom.: 26710 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.550 AC: 83468 AN: 151856 Hom.: 26718 Cov.: 32 AF XY: 0.554 AC XY: 41121 AN XY: 74230

African (AFR) AF: 0.207 AC: 8574 AN: 41356

American (AMR) AF: 0.660 AC: 10076 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3470

East Asian (EAS) AF: 0.932 AC: 4802 AN: 5152

South Asian (SAS) AF: 0.732 AC: 3520 AN: 4810

European-Finnish (FIN) AF: 0.650 AC: 6854 AN: 10544

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.669 AC: 45433 AN: 67946

Other (OTH) AF: 0.594 AC: 1250 AN: 2106

Alfa AF: 0.465 Hom.: 1512

Bravo AF: 0.534

Asia WGS AF: 0.788 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.26
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs3902354; hg19: chr1-109819296;