chr9-134443675-G-A

Variant names:

• chr9-134443675-G-A
• rs3118523
• ENST00000745249.1:n.45G>A

Variant summary

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

The ENST00000745249.1(ENSG00000228877):​n.45G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,016 control chromosomes in the GnomAD database, including 43,053 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 0.75 (43053 hom., cov: 34)
• Consequence: ENSG00000228877 ENST00000745249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 19 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745249.1. 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	ENST00000745249.1		n.45G>A		non_coding_transcript_exon	Exon 1 of 8
	ENSG00000228877	ENST00000745291.1		n.540G>A		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000228877	ENST00000745292.1		n.195G>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113727 AN: 151898 Hom.: 43054 Cov.: 34

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.748 AC: 113762 AN: 152016 Hom.: 43053 Cov.: 34 AF XY: 0.748 AC XY: 55540 AN XY: 74290

African (AFR) AF: 0.646 AC: 26767 AN: 41448

American (AMR) AF: 0.719 AC: 10992 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4083 AN: 5136

South Asian (SAS) AF: 0.560 AC: 2646 AN: 4728

European-Finnish (FIN) AF: 0.867 AC: 9206 AN: 10618

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.808 AC: 54982 AN: 68006

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

Alfa AF: 0.783 Hom.: 21585

Bravo AF: 0.739

Asia WGS AF: 0.653 AC: 2267 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.0
DANN	Benign	0.87
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs3118523; hg19: chr9-137335521; COSMIC: COSV62683936;