rs3866834

Variant names:

• chr4-110822857-G-A
• rs3866834

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 0.284 in 152,010 control chromosomes in the GnomAD database, including 6,975 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 0.28 (6975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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: 0.284 AC: 43103 AN: 151892 Hom.: 6969 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.284 AC: 43107 AN: 152010 Hom.: 6975 Cov.: 32 AF XY: 0.290 AC XY: 21516 AN XY: 74284

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.261

Alfa AF: 0.323 Hom.: 1711

Bravo AF: 0.268

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3866834; hg19: chr4-111744013;