rs17296479

chr5-81411157-T-A

Variant summary

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

The ENST00000670393.1(ENSG00000286721):n.711A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 152,234 control chromosomes in the GnomAD database, including 808 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 0.094 (808 hom., cov: 32)
• Consequence: ENST00000670393.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 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
	ENST00000670393.1	n.711A>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14358 AN: 152116 Hom.: 807 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0943 AC: 14356 AN: 152234 Hom.: 808 Cov.: 32 AF XY: 0.0957 AC XY: 7122 AN XY: 74436

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.0657

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.101 Hom.: 107

Bravo AF: 0.0829

Asia WGS AF: 0.0910 AC: 316 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17296479; hg19: chr5-80706976;