9-119676531-A-T

Variant names:

• chr9-119676531-A-T
• rs17582214
• ENST00000750211.1:n.498-57665T>A

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.498-57665T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,100 control chromosomes in the GnomAD database, including 6,705 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 0.28 (6705 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 2 publications found

Genes affected

ENSG00000297691 (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 (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.498-57665T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43010 AN: 151982 Hom.: 6710 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.283 AC: 43006 AN: 152100 Hom.: 6705 Cov.: 32 AF XY: 0.285 AC XY: 21185 AN XY: 74342

African (AFR) AF: 0.155 AC: 6423 AN: 41526

American (AMR) AF: 0.311 AC: 4749 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3472

East Asian (EAS) AF: 0.162 AC: 836 AN: 5172

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3332 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23640 AN: 67948

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.197 Hom.: 472

Bravo AF: 0.273

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.55
PhyloP100		0.41

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: rs17582214;

hg19: chr9-122438809;