rs72706189

Variant names:

• chr9-11877260-T-C
• rs72706189
• ENST00000649122.1:n.318-50609T>C

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.318-50609T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,092 control chromosomes in the GnomAD database, including 287 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 0.051 (287 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0647 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
ENSG00000285784	ENST00000649122.1	n.318-50609T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0510 AC: 7744 AN: 151976 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0509 AC: 7745 AN: 152092 Hom.: 287 Cov.: 32 AF XY: 0.0530 AC XY: 3939 AN XY: 74338

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0587 Hom.: 73

Bravo AF: 0.0417

Asia WGS AF: 0.0120 AC: 41 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72706189; hg19: chr9-11877260;