chr5-122603459-G-A

Variant names:

• chr5-122603459-G-A
• rs12519633

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 0.144 in 152,098 control chromosomes in the GnomAD database, including 1,960 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 0.14 (1960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.144 AC: 21826 AN: 151980 Hom.: 1946 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.144 AC: 21872 AN: 152098 Hom.: 1960 Cov.: 32 AF XY: 0.145 AC XY: 10788 AN XY: 74356

African (AFR) AF: 0.215 AC: 8900 AN: 41488

American (AMR) AF: 0.148 AC: 2264 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1671 AN: 5160

South Asian (SAS) AF: 0.179 AC: 861 AN: 4818

European-Finnish (FIN) AF: 0.0725 AC: 767 AN: 10578

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.0948 AC: 6445 AN: 68000

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.114 Hom.: 921

Bravo AF: 0.154

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.16
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12519633; hg19: chr5-121939154;