rs3935215

Variant names:

• chr12-55398617-T-A
• rs3935215

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 0.218 in 151,968 control chromosomes in the GnomAD database, including 3,789 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 0.22 (3789 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 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: 0.218 AC: 33062 AN: 151852 Hom.: 3785 Cov.: 30

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.218 AC: 33069 AN: 151968 Hom.: 3789 Cov.: 30 AF XY: 0.215 AC XY: 16011 AN XY: 74298

African (AFR) AF: 0.200 AC: 8285 AN: 41442

American (AMR) AF: 0.207 AC: 3158 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2562 AN: 5144

South Asian (SAS) AF: 0.187 AC: 900 AN: 4812

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10566

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14755 AN: 67952

Other (OTH) AF: 0.233 AC: 490 AN: 2106

Alfa AF: 0.214 Hom.: 441

Bravo AF: 0.223

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.57
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs3935215; hg19: chr12-55792401;