rs3866823

Variant names:

• chr4-110861280-T-A
• rs3866823

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 0.475 in 152,020 control chromosomes in the GnomAD database, including 18,308 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 0.48 (18308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.476 AC: 72264 AN: 151902 Hom.: 18311 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.475 AC: 72265 AN: 152020 Hom.: 18308 Cov.: 32 AF XY: 0.474 AC XY: 35222 AN XY: 74304

African (AFR) AF: 0.293 AC: 12133 AN: 41478

American (AMR) AF: 0.503 AC: 7678 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2251 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2160 AN: 4828

European-Finnish (FIN) AF: 0.536 AC: 5650 AN: 10544

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38596 AN: 67944

Other (OTH) AF: 0.483 AC: 1022 AN: 2114

Alfa AF: 0.519 Hom.: 2642

Bravo AF: 0.465

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs3866823; hg19: chr4-111782436;