8-106912634-A-G

Variant names:

• chr8-106912634-A-G
• rs10504088
• ENST00000766414.1:n.179-12511A>G

Variant summary

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

The ENST00000766414.1(ENSG00000299790):​n.179-12511A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,844 control chromosomes in the GnomAD database, including 32,065 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 0.64 (32065 hom., cov: 32)
• Consequence: ENSG00000299790 ENST00000766414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 0 publications found

Genes affected

ENSG00000299790 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 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
ENSG00000299790	ENST00000766414.1	n.179-12511A>G		intron_variant	Intron 1 of 1
ENSG00000299790	ENST00000766415.1	n.145-12511A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97347 AN: 151724 Hom.: 32042 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.642 AC: 97418 AN: 151844 Hom.: 32065 Cov.: 32 AF XY: 0.634 AC XY: 47067 AN XY: 74208

African (AFR) AF: 0.536 AC: 22210 AN: 41424

American (AMR) AF: 0.567 AC: 8632 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2497 AN: 5156

South Asian (SAS) AF: 0.694 AC: 3345 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6725 AN: 10524

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.728 AC: 49403 AN: 67902

Other (OTH) AF: 0.647 AC: 1367 AN: 2114

Alfa AF: 0.671 Hom.: 4494

Bravo AF: 0.629

Asia WGS AF: 0.553 AC: 1919 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10504088; hg19: chr8-107924862;