rs3934285

Variant names:

• chr1-104056319-G-A
• rs3934285

Your query was ambiguous. Multiple possible variants found:

• chr1-104056319-G-A
• chr1-104056319-G-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 0.242 in 152,068 control chromosomes in the GnomAD database, including 5,224 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 0.24 (5224 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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: 0.243 AC: 36862 AN: 151950 Hom.: 5226 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.242 AC: 36868 AN: 152068 Hom.: 5224 Cov.: 33 AF XY: 0.236 AC XY: 17524 AN XY: 74328

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.278

Alfa AF: 0.311 Hom.: 13268

Bravo AF: 0.243

Asia WGS AF: 0.188 AC: 653 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3934285; hg19: chr1-104598941;