rs7717789

Variant names:

• chr5-29249289-G-A
• rs7717789
• ENST00000651494.1:n.172-7301C>T

Variant summary

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

The ENST00000651494.1(ENSG00000286182):​n.172-7301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,838 control chromosomes in the GnomAD database, including 8,607 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 0.33 (8607 hom., cov: 32)
• Consequence: ENSG00000286182 ENST00000651494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 3 publications found

Genes affected

ENSG00000286182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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
ENSG00000286182	ENST00000651494.1	n.172-7301C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50195 AN: 151720 Hom.: 8602 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.331 AC: 50221 AN: 151838 Hom.: 8607 Cov.: 32 AF XY: 0.329 AC XY: 24405 AN XY: 74188

African (AFR) AF: 0.422 AC: 17477 AN: 41368

American (AMR) AF: 0.307 AC: 4675 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1318 AN: 5140

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2576 AN: 10540

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20730 AN: 67942

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.315 Hom.: 19257

Bravo AF: 0.339

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.28
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs7717789; hg19: chr5-29249396;