6-26239176-A-G

Variant names:

• chr6-26239176-A-G
• rs9358913
• ENST00000707189.1:n.999+115005A>G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+115005A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,132 control chromosomes in the GnomAD database, including 6,775 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 0.25 (6775 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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.999+115005A>G		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1000+81055A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38627 AN: 152012 Hom.: 6770 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.254 AC: 38641 AN: 152132 Hom.: 6775 Cov.: 32 AF XY: 0.269 AC XY: 20005 AN XY: 74360

African (AFR) AF: 0.0582 AC: 2418 AN: 41536

American (AMR) AF: 0.315 AC: 4813 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3468

East Asian (EAS) AF: 0.755 AC: 3907 AN: 5172

South Asian (SAS) AF: 0.442 AC: 2130 AN: 4824

European-Finnish (FIN) AF: 0.442 AC: 4662 AN: 10536

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18574 AN: 67986

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.259 Hom.: 11105

Bravo AF: 0.235

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.46
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs9358913; hg19: chr6-26239404;