5-129838223-T-C

Variant names:

• chr5-129838223-T-C
• rs464316
• ENST00000503616.5:n.121+61238A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515569.1(CHSY3-AS1):​n.132-57742A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 151,804 control chromosomes in the GnomAD database, including 53,323 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 0.83 (53323 hom., cov: 32)
• Consequence: CHSY3-AS1 ENST00000515569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 1 publications found

Genes affected

CHSY3-AS1 (HGNC:58253):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515569.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHSY3-AS1	ENST00000503616.5	TSL:3	n.121+61238A>G		intron	N/A
	CHSY3-AS1	ENST00000515569.1	TSL:2	n.132-57742A>G		intron	N/A
	CHSY3-AS1	ENST00000653455.2		n.149+67357A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125520 AN: 151686 Hom.: 53326 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.827 AC: 125560 AN: 151804 Hom.: 53323 Cov.: 32 AF XY: 0.830 AC XY: 61561 AN XY: 74176

African (AFR) AF: 0.614 AC: 25443 AN: 41434

American (AMR) AF: 0.906 AC: 13804 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3077 AN: 3464

East Asian (EAS) AF: 0.981 AC: 5035 AN: 5132

South Asian (SAS) AF: 0.967 AC: 4665 AN: 4826

European-Finnish (FIN) AF: 0.870 AC: 9200 AN: 10580

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61404 AN: 67834

Other (OTH) AF: 0.862 AC: 1808 AN: 2098

Alfa AF: 0.835 Hom.: 6630

Bravo AF: 0.819

Asia WGS AF: 0.940 AC: 3265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.77
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs464316; hg19: chr5-129173916;