rs9393725

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-67636T>G		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-47154T>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.0881

Gnomad4 FIN AF: 0.0300

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0410

Alfa AF: 0.0277 Hom.: 42

Bravo AF: 0.0446

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9393725; hg19: chr6-26485779;