rs4285229

Variant names:

• chr5-44085326-C-T
• rs4285229

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 0.722 in 152,080 control chromosomes in the GnomAD database, including 39,979 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 0.72 (39979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 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: 0.722 AC: 109666 AN: 151962 Hom.: 39956 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.722 AC: 109730 AN: 152080 Hom.: 39979 Cov.: 32 AF XY: 0.719 AC XY: 53406 AN XY: 74328

African (AFR) AF: 0.731 AC: 30316 AN: 41492

American (AMR) AF: 0.585 AC: 8933 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2700 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2890 AN: 5160

South Asian (SAS) AF: 0.688 AC: 3307 AN: 4806

European-Finnish (FIN) AF: 0.733 AC: 7754 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51363 AN: 67984

Other (OTH) AF: 0.705 AC: 1487 AN: 2110

Alfa AF: 0.741 Hom.: 5639

Bravo AF: 0.708

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.43
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4285229; hg19: chr5-44085428;