rs4285229

Variant names:

• chr5-44085326-C-T
• rs4285229

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 0.722 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.705

Alfa AF: 0.742 Hom.: 5451

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4285229; hg19: chr5-44085428;