9-87354500-T-C

Variant names:

• chr9-87354500-T-C
• rs10217742
• ENST00000690842.2:n.742+30343A>G

Variant summary

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

The ENST00000690842.2(ENSG00000289166):​n.742+30343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,076 control chromosomes in the GnomAD database, including 39,775 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 0.72 (39775 hom., cov: 32)
• Consequence: ENSG00000289166 ENST00000690842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 1 publications found

Genes affected

ENSG00000289166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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
ENSG00000289166	ENST00000690842.2	n.742+30343A>G		intron_variant	Intron 2 of 4
ENSG00000289166	ENST00000804132.1	n.216+32065A>G		intron_variant	Intron 1 of 3
ENSG00000289166	ENST00000804133.1	n.378+30343A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109059 AN: 151958 Hom.: 39726 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.718 AC: 109162 AN: 152076 Hom.: 39775 Cov.: 32 AF XY: 0.714 AC XY: 53091 AN XY: 74332

African (AFR) AF: 0.765 AC: 31766 AN: 41498

American (AMR) AF: 0.614 AC: 9374 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1890 AN: 5152

South Asian (SAS) AF: 0.763 AC: 3671 AN: 4812

European-Finnish (FIN) AF: 0.728 AC: 7702 AN: 10574

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50069 AN: 67980

Other (OTH) AF: 0.682 AC: 1442 AN: 2114

Alfa AF: 0.663 Hom.: 3611

Bravo AF: 0.706

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10217742; hg19: chr9-89969415;