ENST00000690842.2:n.742+40623G>A

Variant names:

• chr9-87344220-C-T
• rs1923782
• ENST00000690842.2:n.742+40623G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000690842.2(ENSG00000289166):​n.742+40623G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,086 control chromosomes in the GnomAD database, including 8,834 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 0.33 (8834 hom., cov: 32)
• Consequence: ENSG00000289166 ENST00000690842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 1 publications found

Genes affected

ENSG00000289166 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690842.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289166	ENST00000690842.2		n.742+40623G>A		intron	N/A
	ENSG00000289166	ENST00000804132.1		n.216+42345G>A		intron	N/A
	ENSG00000289166	ENST00000804133.1		n.378+40623G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50107 AN: 151968 Hom.: 8824 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.330 AC: 50146 AN: 152086 Hom.: 8834 Cov.: 32 AF XY: 0.323 AC XY: 23997 AN XY: 74350

African (AFR) AF: 0.288 AC: 11958 AN: 41484

American (AMR) AF: 0.258 AC: 3936 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3466

East Asian (EAS) AF: 0.0738 AC: 382 AN: 5178

South Asian (SAS) AF: 0.180 AC: 867 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4335 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26431 AN: 67992

Other (OTH) AF: 0.309 AC: 650 AN: 2106

Alfa AF: 0.359 Hom.: 16618

Bravo AF: 0.318

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.69
PhyloP100		0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1923782;

hg19: chr9-89959135;