rs4624820

chr5-142302223-G-A

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 0.545 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.579

Alfa AF: 0.539 Hom.: 51462

Bravo AF: 0.557

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.7
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4624820; hg19: chr5-141681788;