chr8-106924723-G-C

Variant names:

• chr8-106924723-G-C
• rs4236780
• ENST00000766414.1:n.179-422G>C

Variant summary

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

The ENST00000766414.1(ENSG00000299790):​n.179-422G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,056 control chromosomes in the GnomAD database, including 51,035 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 0.82 (51035 hom., cov: 32)
• Consequence: ENSG00000299790 ENST00000766414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 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.179-422G>C		intron_variant	Intron 1 of 1
ENSG00000299790	ENST00000766415.1	n.145-422G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124135 AN: 151938 Hom.: 50981 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.817 AC: 124249 AN: 152056 Hom.: 51035 Cov.: 32 AF XY: 0.810 AC XY: 60189 AN XY: 74278

African (AFR) AF: 0.885 AC: 36754 AN: 41530

American (AMR) AF: 0.742 AC: 11333 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2572 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4090 AN: 5118

South Asian (SAS) AF: 0.824 AC: 3972 AN: 4818

European-Finnish (FIN) AF: 0.724 AC: 7642 AN: 10554

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55185 AN: 67978

Other (OTH) AF: 0.810 AC: 1710 AN: 2112

Alfa AF: 0.810 Hom.: 6212

Bravo AF: 0.821

Asia WGS AF: 0.787 AC: 2738 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	1.1
DANN	Benign	0.49
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs4236780; hg19: chr8-107936951;