rs3866834

Variant names:

• chr4-110822857-G-A
• rs3866834

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 0.284 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

African (AFR) AF: 0.119 AC: 4919 AN: 41478

American (AMR) AF: 0.322 AC: 4912 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1800 AN: 5154

South Asian (SAS) AF: 0.387 AC: 1865 AN: 4822

European-Finnish (FIN) AF: 0.408 AC: 4313 AN: 10560

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23384 AN: 67956

Other (OTH) AF: 0.261 AC: 551 AN: 2108

Alfa AF: 0.321 Hom.: 2872

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
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs3866834; hg19: chr4-111744013;