9-134535779-A-G

Variant names:

• chr9-134535779-A-G
• rs3118594
• ENST00000435284.2:n.103+8495A>G

Variant summary

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

The ENST00000435284.2(ENSG00000228877):​n.103+8495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,786 control chromosomes in the GnomAD database, including 10,587 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 0.37 (10587 hom., cov: 30)
• Consequence: ENSG00000228877 ENST00000435284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-9141A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.2	n.103+8495A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56249 AN: 151668 Hom.: 10573 Cov.: 30

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.371 AC: 56306 AN: 151786 Hom.: 10587 Cov.: 30 AF XY: 0.369 AC XY: 27385 AN XY: 74198

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.400

Alfa AF: 0.362 Hom.: 2022

Bravo AF: 0.369

Asia WGS AF: 0.447 AC: 1555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118594; hg19: chr9-137427625;