rs290278

Variant names:

• chr9-90762564-A-G
• rs290278
• ENST00000831879.1:n.56-19174T>C

Variant summary

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

The ENST00000831879.1(ENSG00000308134):​n.56-19174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,118 control chromosomes in the GnomAD database, including 66,787 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 0.94 (66787 hom., cov: 30)
• Consequence: ENSG00000308134 ENST00000831879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 6 publications found

Genes affected

ENSG00000308134 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000308134	ENST00000831879.1	n.56-19174T>C		intron_variant	Intron 1 of 1
ENSG00000308149	ENST00000831983.1	n.61+5544A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142297 AN: 152000 Hom.: 66734 Cov.: 30

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.936 AC: 142410 AN: 152118 Hom.: 66787 Cov.: 30 AF XY: 0.938 AC XY: 69704 AN XY: 74342

African (AFR) AF: 0.980 AC: 40670 AN: 41506

American (AMR) AF: 0.955 AC: 14601 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3181 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5147 AN: 5152

South Asian (SAS) AF: 0.957 AC: 4607 AN: 4816

European-Finnish (FIN) AF: 0.908 AC: 9612 AN: 10590

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61548 AN: 67988

Other (OTH) AF: 0.946 AC: 1990 AN: 2104

Alfa AF: 0.917 Hom.: 7946

Bravo AF: 0.942

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.50
DANN	Benign	0.34
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs290278; hg19: chr9-93524846;