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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376650	XR_931237.3	n.480+15084T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287984	ENST00000654627.2	n.290+15084T>C		intron_variant	Intron 1 of 2
ENSG00000294396	ENST00000723346.1	n.121+32297A>G		intron_variant	Intron 1 of 1
ENSG00000287984	ENST00000723452.1	n.289+15084T>C		intron_variant	Intron 1 of 2
ENSG00000287984	ENST00000723453.1	n.287-7353T>C		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs17093; hg19: chr11-45045189;