9-134483927-G-T

Variant names:

• chr9-134483927-G-T
• rs3132332
• ENST00000745249.1:n.764+1480G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000745249.1(ENSG00000228877):​n.764+1480G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,984 control chromosomes in the GnomAD database, including 37,040 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 0.68 (37040 hom., cov: 31)
• Consequence: ENSG00000228877 ENST00000745249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 2 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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
ENSG00000228877	ENST00000745249.1	n.764+1480G>T		intron_variant	Intron 5 of 7
ENSG00000228877	ENST00000745250.1	n.195-21544G>T		intron_variant	Intron 2 of 3
ENSG00000228877	ENST00000745251.1	n.672+1480G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103615 AN: 151866 Hom.: 36981 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.683

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.682 AC: 103727 AN: 151984 Hom.: 37040 Cov.: 31 AF XY: 0.679 AC XY: 50389 AN XY: 74240

African (AFR) AF: 0.913 AC: 37863 AN: 41486

American (AMR) AF: 0.567 AC: 8654 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1903 AN: 3464

East Asian (EAS) AF: 0.498 AC: 2557 AN: 5132

South Asian (SAS) AF: 0.644 AC: 3102 AN: 4814

European-Finnish (FIN) AF: 0.611 AC: 6434 AN: 10538

Middle Eastern (MID) AF: 0.686 AC: 199 AN: 290

European-Non Finnish (NFE) AF: 0.605 AC: 41098 AN: 67970

Other (OTH) AF: 0.642 AC: 1353 AN: 2106

Alfa AF: 0.598 Hom.: 11425

Bravo AF: 0.684

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.24
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs3132332; hg19: chr9-137375773;