chr5-26723674-C-A

Variant names:

• chr5-26723674-C-A
• rs4479806
• ENST00000506032.1:n.209+10686G>T

Variant summary

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

The ENST00000506032.1(ENSG00000251033):​n.209+10686G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 152,014 control chromosomes in the GnomAD database, including 738 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 0.080 (738 hom., cov: 32)
• Consequence: ENSG00000251033 ENST00000506032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 12 publications found

Genes affected

ENSG00000251033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 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
ENSG00000251033	ENST00000506032.1	n.209+10686G>T		intron_variant	Intron 2 of 2	3
ENSG00000251033	ENST00000738633.1	n.145-11648G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12187 AN: 151894 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0803 AC: 12210 AN: 152014 Hom.: 738 Cov.: 32 AF XY: 0.0820 AC XY: 6093 AN XY: 74282

African (AFR) AF: 0.0225 AC: 932 AN: 41498

American (AMR) AF: 0.152 AC: 2316 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 325 AN: 3466

East Asian (EAS) AF: 0.234 AC: 1201 AN: 5132

South Asian (SAS) AF: 0.164 AC: 789 AN: 4812

European-Finnish (FIN) AF: 0.0470 AC: 497 AN: 10572

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5762 AN: 67960

Other (OTH) AF: 0.104 AC: 220 AN: 2112

Alfa AF: 0.0909 Hom.: 1891

Bravo AF: 0.0894

Asia WGS AF: 0.200 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs4479806; hg19: chr5-26723783;