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. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.109 AC: 4508 AN: 41500

American (AMR) AF: 0.264 AC: 4029 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5164

South Asian (SAS) AF: 0.130 AC: 626 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2378 AN: 10552

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22211 AN: 67966

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.300 Hom.: 28189

Bravo AF: 0.243

Asia WGS AF: 0.188 AC: 653 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs3934285; hg19: chr1-104598941;