rs3862952

Variant names:

• chr1-211741245-G-A
• rs3862952

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 0.317 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.317 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

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.327

Alfa AF: 0.403 Hom.: 26118

Bravo AF: 0.293

Asia WGS AF: 0.208 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3862952; hg19: chr1-211914587;