chr8-26678069-A-G

Variant names:

• chr8-26678069-A-G
• rs1561817
• ENST00000792407.1:n.85+7195A>G

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.85+7195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,102 control chromosomes in the GnomAD database, including 16,580 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 0.45 (16580 hom., cov: 33)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 6 publications found

Genes affected

ENSG00000303169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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
ENSG00000303169	ENST00000792407.1	n.85+7195A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68887 AN: 151982 Hom.: 16583 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.453 AC: 68901 AN: 152102 Hom.: 16580 Cov.: 33 AF XY: 0.449 AC XY: 33357 AN XY: 74334

African (AFR) AF: 0.339 AC: 14056 AN: 41488

American (AMR) AF: 0.330 AC: 5050 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2583 AN: 5168

South Asian (SAS) AF: 0.338 AC: 1628 AN: 4820

European-Finnish (FIN) AF: 0.588 AC: 6208 AN: 10564

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36219 AN: 67986

Other (OTH) AF: 0.426 AC: 901 AN: 2114

Alfa AF: 0.504 Hom.: 11705

Bravo AF: 0.432

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs1561817; hg19: chr8-26535586;