5-136736365-G-A

Variant names:

• chr5-136736365-G-A
• rs726846
• ENST00000502421.2:n.79+1360G>A

Variant summary

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

The ENST00000502421.2(CTB-1I21.1):​n.79+1360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,084 control chromosomes in the GnomAD database, including 15,891 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 0.45 (15891 hom., cov: 33)
• Consequence: CTB-1I21.1 ENST00000502421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

Genes affected

CTB-1I21.1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTB-1I21.1	NR_188336.1		n.75+1360G>A		intron	N/A
	CTB-1I21.1	NR_188337.1		n.75+1360G>A		intron	N/A
	CTB-1I21.1	NR_188338.1		n.75+1360G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTB-1I21.1	ENST00000502421.2	TSL:4	n.79+1360G>A		intron	N/A
	CTB-1I21.1	ENST00000656447.1		n.75+1360G>A		intron	N/A
	CTB-1I21.1	ENST00000662288.1		n.176+1360G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68845 AN: 151966 Hom.: 15885 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.453 AC: 68874 AN: 152084 Hom.: 15891 Cov.: 33 AF XY: 0.451 AC XY: 33566 AN XY: 74344

African (AFR) AF: 0.404 AC: 16776 AN: 41498

American (AMR) AF: 0.444 AC: 6794 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3464

East Asian (EAS) AF: 0.690 AC: 3559 AN: 5160

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4826

European-Finnish (FIN) AF: 0.423 AC: 4464 AN: 10560

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32219 AN: 67976

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.423 Hom.: 4279

Bravo AF: 0.456

Asia WGS AF: 0.519 AC: 1803 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	0.27
DANN	Benign	0.27
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs726846; hg19: chr5-136072054;