rs748964

Variant names:

• chr9-134442243-C-G
• rs748964
• ENST00000745272.1:n.-4C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-134442243-C-G
• chr9-134442243-C-T

Variant summary

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

The ENST00000745272.1(ENSG00000228877):​n.-4C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,286 control chromosomes in the GnomAD database, including 59,814 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 0.88 (59814 hom., cov: 34)
• Consequence: ENSG00000228877 ENST00000745272.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228877	ENST00000745272.1		n.-4C>G		upstream_gene	N/A
	ENSG00000228877	ENST00000745291.1		n.-4C>G		upstream_gene	N/A
	ENSG00000228877	ENST00000745292.1		n.-165C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134544 AN: 152168 Hom.: 59773 Cov.: 34

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.884 AC: 134641 AN: 152286 Hom.: 59814 Cov.: 34 AF XY: 0.882 AC XY: 65678 AN XY: 74454

African (AFR) AF: 0.961 AC: 39948 AN: 41570

American (AMR) AF: 0.829 AC: 12689 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2932 AN: 3470

East Asian (EAS) AF: 0.824 AC: 4264 AN: 5172

South Asian (SAS) AF: 0.700 AC: 3378 AN: 4824

European-Finnish (FIN) AF: 0.912 AC: 9683 AN: 10618

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58966 AN: 68008

Other (OTH) AF: 0.846 AC: 1788 AN: 2114

Alfa AF: 0.881 Hom.: 6875

Bravo AF: 0.883

Asia WGS AF: 0.785 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.39
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs748964; hg19: chr9-137334089; COSMIC: COSV62683935;