rs4479806

chr5-26723674-C-Achr5-26723674-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506032.1(ENSG00000251033):n.209+10686G>T variant causes a intron, non coding transcript 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: ENST00000506032.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506032.1	n.209+10686G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0938

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0848

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0919 Hom.: 1384

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4479806; hg19: chr5-26723783;