5-121573083-G-A

Variant names:

• chr5-121573083-G-A
• rs4559029

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 0.514 in 151,974 control chromosomes in the GnomAD database, including 21,096 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 0.51 (21096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.514 AC: 78060 AN: 151856 Hom.: 21069 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.514 AC: 78112 AN: 151974 Hom.: 21096 Cov.: 32 AF XY: 0.515 AC XY: 38225 AN XY: 74248

African (AFR) AF: 0.352 AC: 14611 AN: 41456

American (AMR) AF: 0.564 AC: 8609 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3466

East Asian (EAS) AF: 0.830 AC: 4264 AN: 5140

South Asian (SAS) AF: 0.553 AC: 2660 AN: 4814

European-Finnish (FIN) AF: 0.537 AC: 5663 AN: 10536

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38498 AN: 67970

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.550 Hom.: 73307

Bravo AF: 0.513

Asia WGS AF: 0.665 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs4559029; hg19: chr5-120908778;