5-121233616-T-C

Variant names:

• chr5-121233616-T-C
• rs2973413
• ENST00000599562.5:n.228+28486T>C

Variant summary

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

The ENST00000599562.5(ENSG00000229855):​n.228+28486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,074 control chromosomes in the GnomAD database, including 46,843 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 0.78 (46843 hom., cov: 32)
• Consequence: ENSG00000229855 ENST00000599562.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.85 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+28486T>C		intron_variant	Intron 2 of 5	5
ENSG00000229855	ENST00000661647.1	n.195+68735T>C		intron_variant	Intron 1 of 2
ENSG00000229855	ENST00000767774.1	n.85+68735T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118205 AN: 151956 Hom.: 46829 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.778 AC: 118263 AN: 152074 Hom.: 46843 Cov.: 32 AF XY: 0.778 AC XY: 57795 AN XY: 74328

African (AFR) AF: 0.621 AC: 25747 AN: 41448

American (AMR) AF: 0.781 AC: 11945 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3187 AN: 3472

East Asian (EAS) AF: 0.690 AC: 3567 AN: 5170

South Asian (SAS) AF: 0.861 AC: 4156 AN: 4826

European-Finnish (FIN) AF: 0.821 AC: 8683 AN: 10582

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58170 AN: 67980

Other (OTH) AF: 0.792 AC: 1667 AN: 2106

Alfa AF: 0.832 Hom.: 27688

Bravo AF: 0.766

Asia WGS AF: 0.777 AC: 2694 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2973413; hg19: chr5-120569311;