rs7717789

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.326

Alfa AF: 0.306 Hom.: 9894

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7717789; hg19: chr5-29249396;