rs3862952

Variant names:

• chr1-211741245-G-A
• rs3862952

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 0.317 in 151,860 control chromosomes in the GnomAD database, including 9,016 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 0.32 (9016 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.317 AC: 48177 AN: 151744 Hom.: 9016 Cov.: 30

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.0573

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.317 AC: 48178 AN: 151860 Hom.: 9016 Cov.: 30 AF XY: 0.315 AC XY: 23369 AN XY: 74202

African (AFR) AF: 0.160 AC: 6633 AN: 41438

American (AMR) AF: 0.238 AC: 3626 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3468

East Asian (EAS) AF: 0.0574 AC: 297 AN: 5172

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4810

European-Finnish (FIN) AF: 0.418 AC: 4392 AN: 10506

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.430 AC: 29225 AN: 67890

Other (OTH) AF: 0.327 AC: 690 AN: 2108

Alfa AF: 0.390 Hom.: 52562

Bravo AF: 0.293

Asia WGS AF: 0.208 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs3862952; hg19: chr1-211914587;