9-134444068-C-G

Variant names:

• chr9-134444068-C-G
• rs1007971
• ENST00000745249.1:n.123+315C>G

Variant summary

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

The ENST00000745249.1(ENSG00000228877):​n.123+315C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,906 control chromosomes in the GnomAD database, including 36,108 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 0.67 (36108 hom., cov: 30)
• Consequence: ENSG00000228877 ENST00000745249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 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.123+315C>G		intron_variant	Intron 1 of 7
ENSG00000228877	ENST00000745250.1	n.106+278C>G		intron_variant	Intron 1 of 3
ENSG00000228877	ENST00000745272.1	n.235-1165C>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101659 AN: 151790 Hom.: 36110 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.669 AC: 101687 AN: 151906 Hom.: 36108 Cov.: 30 AF XY: 0.672 AC XY: 49878 AN XY: 74232

African (AFR) AF: 0.428 AC: 17724 AN: 41386

American (AMR) AF: 0.664 AC: 10135 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2709 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3421 AN: 5132

South Asian (SAS) AF: 0.547 AC: 2633 AN: 4812

European-Finnish (FIN) AF: 0.830 AC: 8782 AN: 10576

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54043 AN: 67946

Other (OTH) AF: 0.669 AC: 1414 AN: 2114

Alfa AF: 0.673 Hom.: 2292

Bravo AF: 0.650

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1007971; hg19: chr9-137335914; COSMIC: COSV62683938;