9-134535596-T-C

Variant names:

• chr9-134535596-T-C
• rs3132315
• ENST00000435284.2:n.103+8312T>C

Variant summary

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

The ENST00000435284.2(ENSG00000228877):​n.103+8312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,088 control chromosomes in the GnomAD database, including 47,028 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 0.78 (47028 hom., cov: 33)
• Consequence: ENSG00000228877 ENST00000435284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-9324T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.2	n.103+8312T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118869 AN: 151970 Hom.: 46985 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.782 AC: 118973 AN: 152088 Hom.: 47028 Cov.: 33 AF XY: 0.778 AC XY: 57875 AN XY: 74346

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.799

Alfa AF: 0.754 Hom.: 57940

Bravo AF: 0.801

Asia WGS AF: 0.803 AC: 2788 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	0.82
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132315; hg19: chr9-137427442;