ENST00000668681.2:n.572-4412A>G

Variant names:

• chr9-7919153-T-C
• rs2208742
• ENST00000668681.2:n.572-4412A>G

Variant summary

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

The ENST00000668681.2(ENSG00000231902):​n.572-4412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,176 control chromosomes in the GnomAD database, including 52,400 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 0.83 (52400 hom., cov: 32)
• Consequence: ENSG00000231902 ENST00000668681.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 0 publications found

Genes affected

ENSG00000231902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668681.2. 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
	ENSG00000231902	ENST00000668681.2		n.572-4412A>G		intron	N/A
	ENSG00000231902	ENST00000813700.1		n.569-497A>G		intron	N/A
	ENSG00000231902	ENST00000813701.1		n.768-4412A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125703 AN: 152058 Hom.: 52350 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.827 AC: 125814 AN: 152176 Hom.: 52400 Cov.: 32 AF XY: 0.826 AC XY: 61429 AN XY: 74374

African (AFR) AF: 0.923 AC: 38335 AN: 41546

American (AMR) AF: 0.818 AC: 12486 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2454 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4982 AN: 5176

South Asian (SAS) AF: 0.824 AC: 3976 AN: 4824

European-Finnish (FIN) AF: 0.777 AC: 8215 AN: 10570

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.775 AC: 52680 AN: 68000

Other (OTH) AF: 0.805 AC: 1702 AN: 2114

Alfa AF: 0.781 Hom.: 79032

Bravo AF: 0.835

Asia WGS AF: 0.890 AC: 3093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2208742; hg19: chr9-7919153;