5-121229828-C-T

Variant names:

• chr5-121229828-C-T
• rs919289
• ENST00000599562.5:n.228+24698C>T

Variant summary

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

The ENST00000599562.5(ENSG00000229855):​n.228+24698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,886 control chromosomes in the GnomAD database, including 43,697 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 0.75 (43697 hom., cov: 30)
• Consequence: ENSG00000229855 ENST00000599562.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000229855 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.834 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
ENSG00000229855	ENST00000599562.5	n.228+24698C>T		intron_variant	Intron 2 of 5	5
ENSG00000229855	ENST00000661647.1	n.195+64947C>T		intron_variant	Intron 1 of 2
ENSG00000229855	ENST00000767774.1	n.85+64947C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113567 AN: 151768 Hom.: 43688 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.748 AC: 113618 AN: 151886 Hom.: 43697 Cov.: 30 AF XY: 0.748 AC XY: 55485 AN XY: 74226

African (AFR) AF: 0.556 AC: 23010 AN: 41354

American (AMR) AF: 0.769 AC: 11751 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3150 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3468 AN: 5132

South Asian (SAS) AF: 0.855 AC: 4122 AN: 4820

European-Finnish (FIN) AF: 0.783 AC: 8257 AN: 10548

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57094 AN: 67970

Other (OTH) AF: 0.770 AC: 1627 AN: 2112

Alfa AF: 0.820 Hom.: 26040

Bravo AF: 0.736

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs919289; hg19: chr5-120565523;