ENST00000707189.1:n.999+86969A>G

Variant names:

• chr6-26211140-A-G
• rs11755943
• ENST00000707189.1:n.999+86969A>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+86969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,224 control chromosomes in the GnomAD database, including 2,318 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 0.17 (2318 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 15 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 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+86969A>G		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1000+53019A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25478 AN: 152106 Hom.: 2321 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.167 AC: 25484 AN: 152224 Hom.: 2318 Cov.: 32 AF XY: 0.168 AC XY: 12486 AN XY: 74412

African (AFR) AF: 0.231 AC: 9578 AN: 41516

American (AMR) AF: 0.152 AC: 2323 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.110 AC: 569 AN: 5184

South Asian (SAS) AF: 0.229 AC: 1106 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10606

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

European-Non Finnish (NFE) AF: 0.138 AC: 9368 AN: 68004

Other (OTH) AF: 0.178 AC: 376 AN: 2114

Alfa AF: 0.150 Hom.: 3079

Bravo AF: 0.169

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11755943; hg19: chr6-26211368;