8-80321732-T-C

Variant names:

• chr8-80321732-T-C
• rs10090469
• ENST00000522044.1:n.405-18069T>C

Variant summary

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

The ENST00000522044.1(ENSG00000253238):​n.405-18069T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,230 control chromosomes in the GnomAD database, including 58,271 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 0.87 (58271 hom., cov: 32)
• Consequence: ENSG00000253238 ENST00000522044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 4 publications found

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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
ENSG00000253238	ENST00000522044.1	n.405-18069T>C		intron_variant	Intron 3 of 3	3
ENSG00000253238	ENST00000644465.1	n.253+32730T>C		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656068.1	n.392-14316T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132440 AN: 152112 Hom.: 58212 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.871 AC: 132554 AN: 152230 Hom.: 58271 Cov.: 32 AF XY: 0.867 AC XY: 64503 AN XY: 74426

African (AFR) AF: 0.971 AC: 40346 AN: 41556

American (AMR) AF: 0.796 AC: 12157 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2974 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3035 AN: 5182

South Asian (SAS) AF: 0.765 AC: 3687 AN: 4822

European-Finnish (FIN) AF: 0.862 AC: 9122 AN: 10582

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58349 AN: 68022

Other (OTH) AF: 0.869 AC: 1834 AN: 2110

Alfa AF: 0.845 Hom.: 35274

Bravo AF: 0.866

Asia WGS AF: 0.697 AC: 2421 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.50
DANN	Benign	0.74
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10090469; hg19: chr8-81233967;