rs9393725

Variant names:

• chr6-26485551-T-G
• rs9393725
• ENST00000707189.1:n.1000-67636T>G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-67636T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 150,618 control chromosomes in the GnomAD database, including 257 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 0.044 (257 hom., cov: 30)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 2 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. 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
	ENSG00000291336	ENST00000707189.1		n.1000-67636T>G		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1001-47154T>G		intron	N/A
	ENSG00000300236	ENST00000770281.1		n.558+2166A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0439 AC: 6606 AN: 150498 Hom.: 257 Cov.: 30

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0405

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

GnomAD4 genome AF: 0.0439 AC: 6617 AN: 150618 Hom.: 257 Cov.: 30 AF XY: 0.0446 AC XY: 3277 AN XY: 73482

African (AFR) AF: 0.0922 AC: 3787 AN: 41088

American (AMR) AF: 0.0179 AC: 270 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3458

East Asian (EAS) AF: 0.0906 AC: 458 AN: 5054

South Asian (SAS) AF: 0.0881 AC: 420 AN: 4768

European-Finnish (FIN) AF: 0.0300 AC: 305 AN: 10150

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0177 AC: 1196 AN: 67686

Other (OTH) AF: 0.0410 AC: 86 AN: 2096

Alfa AF: 0.0283 Hom.: 55

Bravo AF: 0.0446

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.52
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs9393725; hg19: chr6-26485779;