ENST00000780084.1:n.192+25690A>G

Variant names:

• chr6-121793305-A-G
• rs9320841
• ENST00000780084.1:n.192+25690A>G

Variant summary

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

The ENST00000780084.1(ENSG00000289871):​n.192+25690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,092 control chromosomes in the GnomAD database, including 6,782 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 0.23 (6782 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 9 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377979	XR_942936.3	n.237+25690A>G		intron_variant	Intron 1 of 6
LOC105377979	XR_942937.4	n.237+25690A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289871	ENST00000780084.1	n.192+25690A>G		intron_variant	Intron 1 of 4
ENSG00000289871	ENST00000780085.1	n.79+25690A>G		intron_variant	Intron 1 of 3
ENSG00000289871	ENST00000780086.1	n.108+25690A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35021 AN: 151974 Hom.: 6744 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.231 AC: 35106 AN: 152092 Hom.: 6782 Cov.: 32 AF XY: 0.229 AC XY: 17055 AN XY: 74338

African (AFR) AF: 0.518 AC: 21460 AN: 41438

American (AMR) AF: 0.121 AC: 1850 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0977 AC: 339 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2267 AN: 5172

South Asian (SAS) AF: 0.107 AC: 519 AN: 4828

European-Finnish (FIN) AF: 0.131 AC: 1391 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0998 AC: 6791 AN: 68012

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.164 Hom.: 5912

Bravo AF: 0.244

Asia WGS AF: 0.298 AC: 1035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs9320841; hg19: chr6-122114451;