rs72706189

chr9-11877260-T-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, non coding transcript 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: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649122.1	n.318-50609T>C		intron_variant, non_coding_transcript_variant

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;