8-26720128-C-T

Variant names:

• chr8-26720128-C-T
• rs73229635
• ENST00000792407.1:n.86-12168C>T

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.86-12168C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,178 control chromosomes in the GnomAD database, including 171 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 0.038 (171 hom., cov: 30)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 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.86-12168C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5763 AN: 152060 Hom.: 171 Cov.: 30

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0378 AC: 5759 AN: 152178 Hom.: 171 Cov.: 30 AF XY: 0.0373 AC XY: 2774 AN XY: 74410

African (AFR) AF: 0.0110 AC: 456 AN: 41514

American (AMR) AF: 0.0403 AC: 616 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4820

European-Finnish (FIN) AF: 0.0385 AC: 408 AN: 10596

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0543 AC: 3694 AN: 68004

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0204 Hom.: 9

Bravo AF: 0.0376

Asia WGS AF: 0.0120 AC: 42 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	0.30
DANN	Benign	0.59
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs73229635; hg19: chr8-26577645;