5-142302223-G-A

Variant names:

• chr5-142302223-G-A
• rs4624820

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 0.545 in 151,936 control chromosomes in the GnomAD database, including 22,890 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 0.55 (22890 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82832 AN: 151818 Hom.: 22885 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.545 AC: 82878 AN: 151936 Hom.: 22890 Cov.: 31 AF XY: 0.542 AC XY: 40276 AN XY: 74258

African (AFR) AF: 0.597 AC: 24732 AN: 41424

American (AMR) AF: 0.592 AC: 9046 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2190 AN: 3466

East Asian (EAS) AF: 0.295 AC: 1520 AN: 5160

South Asian (SAS) AF: 0.500 AC: 2410 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4849 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36290 AN: 67948

Other (OTH) AF: 0.579 AC: 1219 AN: 2104

Alfa AF: 0.539 Hom.: 107486

Bravo AF: 0.557

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.65
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs4624820; hg19: chr5-141681788;