9-7918996-A-G

Variant names:

• chr9-7918996-A-G
• rs2224601
• ENST00000668681.2:n.572-4255T>C

Variant summary

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

The ENST00000668681.2(ENSG00000231902):​n.572-4255T>C 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 152,244 control chromosomes in the GnomAD database, including 52,513 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 (52513 hom., cov: 33)
• Consequence: ENSG00000231902 ENST00000668681.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• 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=-0.96).
• 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231902	ENST00000668681.2		n.572-4255T>C		intron	N/A
	ENSG00000231902	ENST00000813700.1		n.569-340T>C		intron	N/A
	ENSG00000231902	ENST00000813701.1		n.768-4255T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125865 AN: 152126 Hom.: 52464 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.827 AC: 125974 AN: 152244 Hom.: 52513 Cov.: 33 AF XY: 0.827 AC XY: 61550 AN XY: 74430

African (AFR) AF: 0.923 AC: 38339 AN: 41550

American (AMR) AF: 0.823 AC: 12568 AN: 15280

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

East Asian (EAS) AF: 0.963 AC: 4983 AN: 5176

South Asian (SAS) AF: 0.826 AC: 3984 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8242 AN: 10604

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52715 AN: 68020

Other (OTH) AF: 0.806 AC: 1704 AN: 2114

Alfa AF: 0.788 Hom.: 199748

Bravo AF: 0.836

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.34
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2224601; hg19: chr9-7918996;