5-129838223-T-C

Position:

• chr5-129838223-T-C

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 0.827 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129838223T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251680	ENST00000503616.5	n.121+61238A>G		intron_variant		3
ENSG00000251680	ENST00000515569.1	n.132-57742A>G		intron_variant		2
ENSG00000251680	ENST00000653455.1	n.93+67357A>G		intron_variant

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

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.862

Alfa AF: 0.844 Hom.: 6483

Bravo AF: 0.819

Asia WGS AF: 0.940 AC: 3265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs464316; hg19: chr5-129173916;