8-69897026-T-C

Variant names:

• chr8-69897026-T-C
• rs12680109
• ENST00000822047.1:n.355-4116A>G

Variant summary

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

The ENST00000822047.1(ENSG00000306926):​n.355-4116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,050 control chromosomes in the GnomAD database, including 11,821 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 0.39 (11821 hom., cov: 32)
• Consequence: ENSG00000306926 ENST00000822047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948
• Publications: 5 publications found

Genes affected

ENSG00000306926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306926	ENST00000822047.1	n.355-4116A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59410 AN: 151934 Hom.: 11826 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.391 AC: 59429 AN: 152050 Hom.: 11821 Cov.: 32 AF XY: 0.395 AC XY: 29338 AN XY: 74310

African (AFR) AF: 0.290 AC: 12009 AN: 41470

American (AMR) AF: 0.466 AC: 7111 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2733 AN: 5170

South Asian (SAS) AF: 0.440 AC: 2124 AN: 4824

European-Finnish (FIN) AF: 0.448 AC: 4727 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28012 AN: 67974

Other (OTH) AF: 0.403 AC: 848 AN: 2104

Alfa AF: 0.399 Hom.: 21981

Bravo AF: 0.390

Asia WGS AF: 0.496 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.68
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs12680109; hg19: chr8-70809261;