rs529820

Variant names:

• chr9-87925720-C-T
• rs529820
• ENST00000783875.1:n.174+7409G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000783875.1(ENSG00000289459):​n.174+7409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 148,900 control chromosomes in the GnomAD database, including 3 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 0.0027 (3 hom., cov: 30)
• Consequence: ENSG00000289459 ENST00000783875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 1 publications found

Genes affected

ENSG00000289459 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC497256	NR_149022.1	n.472+7409G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289459	ENST00000783875.1	n.174+7409G>A		intron_variant	Intron 3 of 3
ENSG00000289459	ENST00000783876.1	n.347+7409G>A		intron_variant	Intron 3 of 4
ENSG00000289459	ENST00000783877.1	n.509+7409G>A		intron_variant	Intron 3 of 3
ENSG00000289459	ENST00000783878.1	n.353+5337G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.00272 AC: 405 AN: 148788 Hom.: 3 Cov.: 30

Gnomad AFR AF: 0.00971

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000936

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000650

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000738

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00272 AC: 405 AN: 148900 Hom.: 3 Cov.: 30 AF XY: 0.00257 AC XY: 187 AN XY: 72688

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00968 AC: 383 AN: 39574

American (AMR) AF: 0.000934 AC: 14 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3440

East Asian (EAS) AF: 0.000652 AC: 3 AN: 4602

South Asian (SAS) AF: 0.00 AC: 0 AN: 4704

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10546

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000738 AC: 5 AN: 67772

Other (OTH) AF: 0.00 AC: 0 AN: 2076

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00413 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.35
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs529820; hg19: chr9-90540635; COSMIC: COSV69665997;