rs17093

Variant names:

• chr11-45023638-T-C
• rs17093
• ENST00000654627.2:n.290+15084T>C

Variant summary

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

The ENST00000654627.2(ENSG00000287984):​n.290+15084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,096 control chromosomes in the GnomAD database, including 2,438 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 0.18 (2438 hom., cov: 31)
• Consequence: ENSG00000287984 ENST00000654627.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 5 publications found

Genes affected

ENSG00000287984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654627.2. 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
	ENSG00000287984	ENST00000654627.2		n.290+15084T>C		intron	N/A
	ENSG00000294396	ENST00000723346.1		n.121+32297A>G		intron	N/A
	ENSG00000287984	ENST00000723452.1		n.289+15084T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26709 AN: 151978 Hom.: 2439 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.176 AC: 26714 AN: 152096 Hom.: 2438 Cov.: 31 AF XY: 0.172 AC XY: 12762 AN XY: 74358

African (AFR) AF: 0.195 AC: 8088 AN: 41462

American (AMR) AF: 0.152 AC: 2319 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.0868 AC: 448 AN: 5160

South Asian (SAS) AF: 0.108 AC: 521 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1771 AN: 10588

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12397 AN: 67986

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.180 Hom.: 7614

Bravo AF: 0.178

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.36
PhyloP100		0.48

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: rs17093;

hg19: chr11-45045189;