8-59710789-A-C

Variant names:

• chr8-59710789-A-C
• rs12541902
• ENST00000796877.1:n.163-4089A>C

Variant summary

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

The ENST00000796877.1(ENSG00000303742):​n.163-4089A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,938 control chromosomes in the GnomAD database, including 40,070 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 0.72 (40070 hom., cov: 30)
• Consequence: ENSG00000303742 ENST00000796877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 5 publications found

Genes affected

ENSG00000303742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796877.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303742	ENST00000796877.1		n.163-4089A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110021 AN: 151818 Hom.: 40040 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.725 AC: 110105 AN: 151938 Hom.: 40070 Cov.: 30 AF XY: 0.728 AC XY: 54082 AN XY: 74280

African (AFR) AF: 0.729 AC: 30206 AN: 41414

American (AMR) AF: 0.775 AC: 11832 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2297 AN: 3468

East Asian (EAS) AF: 0.956 AC: 4926 AN: 5152

South Asian (SAS) AF: 0.751 AC: 3609 AN: 4808

European-Finnish (FIN) AF: 0.723 AC: 7637 AN: 10564

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47338 AN: 67954

Other (OTH) AF: 0.727 AC: 1531 AN: 2106

Alfa AF: 0.705 Hom.: 95875

Bravo AF: 0.729

Asia WGS AF: 0.837 AC: 2911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.72
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12541902; hg19: chr8-60623348;